@graphty/graph-io 0.3.28 → 0.3.30

package/dist/chunks/exporter-DhtW6FxK.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"exporter-DhtW6FxK.js","sources":["../../src/formats/obo/syntax.ts","../../src/formats/obo/importer.ts","../../src/formats/obo/exporter.ts"],"sourcesContent":["/**\n * The lexical layer of the OBO importer (research-obo.md section 4.1): the tag-value line, the\n * hidden `!` comment, the trailing `{name=\"value\", ...}` qualifier block, the escapes of the OBO\n * guides, quoted strings and bracketed xref lists. Pure functions over one logical line; the\n * importer joins backslash continuations and splits form feeds before calling them.\n *\n * Every function works on the RAW text (escapes still in place) and unescapes only the pieces it\n * hands back, so an escaped quote, colon, comma, brace or `!` never ends a construct.\n */\n\n/** The OBO escapes with a meaning of their own; any other `\\x` is `x` (the guides). */\nconst ESCAPES: Readonly<Record<string, string>> = Object.freeze({\n    n: \"\\n\",\n    t: \"\\t\",\n    // the guides read `\\W` as a space; the 1.4 BNF (and fastobo) as the letter W (design 4.1)\n    W: \" \",\n});\n\n/**\n * Remove the OBO escapes: `\\n` newline, `\\t` tab, `\\W` space, any other `\\x` the character x; a\n * backslash at the very end is dropped.\n * @param text - raw text\n * @returns the unescaped text\n * @category Plugin helpers\n */\nexport function unescapeObo(text: string): string {\n    if (!text.includes(\"\\\\\")) {\n        return text;\n    }\n    let out = \"\";\n    for (let i = 0; i < text.length; i++) {\n        const ch = text[i];\n        if (ch !== \"\\\\\") {\n            out += ch;\n            continue;\n        }\n        i++;\n        if (i < text.length) {\n            const next = text[i];\n            out += ESCAPES[next] ?? next;\n        }\n    }\n    return out;\n}\n\n/**\n * Whether the character at `index` is escaped (preceded by an odd run of backslashes).\n * @param text - the text\n * @param index - the character's index\n * @returns true when escaped\n */\nfunction isEscaped(text: string, index: number): boolean {\n    let run = 0;\n    for (let i = index - 1; i >= 0 && text[i] === \"\\\\\"; i--) {\n        run++;\n    }\n    return run % 2 === 1;\n}\n\n/**\n * Split a line at the form feeds outside quotes (the 1.4 grammar counts a form feed as a line end;\n * one inside a quoted value is text).\n * @param line - the raw line\n * @returns the pieces, the line itself when it holds no such form feed\n * @category Plugin helpers\n */\nexport function splitFormFeeds(line: string): string[] {\n    if (!line.includes(\"\\f\")) {\n        return [line];\n    }\n    const pieces: string[] = [];\n    let quoted = false;\n    let start = 0;\n    for (let i = 0; i < line.length; i += line[i] === \"\\\\\" ? 2 : 1) {\n        const ch = line[i];\n        if (ch === '\"') {\n            quoted = !quoted;\n        } else if (ch === \"\\f\" && !quoted) {\n            pieces.push(line.slice(start, i));\n            start = i + 1;\n        }\n    }\n    pieces.push(line.slice(start));\n    return pieces;\n}\n\n/**\n * Whether a raw line ends with an unescaped backslash (the 1.0 / 1.2 line continuation).\n * @param line - the raw line, trailing whitespace included\n * @returns true when the line continues on the next one\n * @category Plugin helpers\n */\nexport function endsWithContinuation(line: string): boolean {\n    return line.endsWith(\"\\\\\") && !isEscaped(line, line.length - 1);\n}\n\n/** A tag-value line split at its first unescaped colon. */\ninterface TagValue {\n    /** The tag, unescaped and trimmed. */\n    readonly tag: string;\n    /** The raw text after the colon, leading whitespace removed. */\n    readonly rest: string;\n}\n\n/**\n * Split a line at its first unescaped colon (values contain colons freely: `is_a: GO:0000001`).\n * @param line - the raw line, trimmed\n * @returns the tag and the rest, or null when the line has no colon\n * @category Plugin helpers\n */\nexport function splitTagValue(line: string): TagValue | null {\n    for (let i = 0; i < line.length; i++) {\n        if (line[i] === \"\\\\\") {\n            i++;\n            continue;\n        }\n        if (line[i] === \":\") {\n            return { tag: unescapeObo(line.slice(0, i).trim()), rest: line.slice(i + 1).trimStart() };\n        }\n    }\n    return null;\n}\n\n/**\n * Strip the hidden comment: an unescaped `!` outside quotes that starts the value or follows\n * whitespace begins a comment running to the end of the line. A `!` glued to the text before it\n * (`#!/`, `Hello!`) is text, so URLs and names are never cut. A quote opens a string only where a\n * token starts, as tokenize() reads it, so the `\"` of an unquoted `5\" pipe` is text and does not\n * hide the comment after it.\n * @param rest - the raw value\n * @returns the value before the comment, trailing whitespace removed\n * @category Plugin helpers\n */\nexport function stripComment(rest: string): string {\n    let quoted = false;\n    for (let i = 0; i < rest.length; i++) {\n        const ch = rest[i];\n        if (ch === \"\\\\\") {\n            i++;\n            continue;\n        }\n        const atStart = i === 0 || rest[i - 1] === \" \" || rest[i - 1] === \"\\t\";\n        if (ch === '\"' && (quoted || atStart)) {\n            quoted = !quoted;\n        } else if (ch === \"!\" && !quoted && atStart) {\n            return rest.slice(0, i).trimEnd();\n        }\n    }\n    return rest.trimEnd();\n}\n\n/**\n * The qualifiers of a clause: name to value (a list when a name repeats).\n * @category Plugin helpers\n */\nexport type Qualifiers = Record<string, string | string[]>;\n\n/** A value with its trailing qualifier blocks split off. */\ninterface QualifiedValue {\n    /** The raw value without the blocks, trimmed. */\n    readonly value: string;\n    /** The qualifiers, or null when the value has none. */\n    readonly qualifiers: Qualifiers | null;\n    /** A block that closes the value but does not parse, kept in `value` as text. */\n    readonly badBlock: string | null;\n}\n\n/**\n * Split the trailing qualifier blocks off a value: a `{...}` is a block only when it closes the\n * value (after the comment was stripped); several blocks (`{a=\"1\"}{b=\"2\"}`, 1.2 examples) are\n * merged. A closing brace whose block does not parse is left in the value and reported. The value\n * is scanned once, so a value of many blocks costs its length, not its length times its blocks.\n * @param value - the raw value without its comment\n * @returns the value and its qualifiers\n * @category Plugin helpers\n */\nexport function splitQualifiers(value: string): QualifiedValue {\n    if (!value.endsWith(\"}\")) {\n        return { value, qualifiers: null, badBlock: null };\n    }\n    const blocks = braceBlocks(value);\n    // the blocks read right to left, merged left to right below\n    const parsed: Qualifiers[] = [];\n    let end = value.length;\n    let badBlock: string | null = null;\n    while (end > 0 && value[end - 1] === \"}\" && !isEscaped(value, end - 1)) {\n        const open = blocks.get(end - 1) ?? -1;\n        const block = open < 0 ? null : parseQualifiers(value.slice(open + 1, end - 1));\n        if (block === null) {\n            badBlock = value.slice(Math.max(open, 0), end);\n            break;\n        }\n        parsed.push(block);\n        end = open;\n        while (end > 0 && /\\s/.test(value[end - 1])) {\n            end--;\n        }\n    }\n    let qualifiers: Qualifiers | null = null;\n    for (let i = parsed.length - 1; i >= 0; i--) {\n        qualifiers ??= Object.create(null) as Qualifiers;\n        for (const [name, v] of Object.entries(parsed[i])) {\n            addQualifier(qualifiers, name, v);\n        }\n    }\n    return { value: value.slice(0, end), qualifiers, badBlock };\n}\n\n/**\n * The qualifier blocks of a value in one scan: for every unescaped `}` outside quotes, the index of\n * the unescaped `{` outside quotes that opens it (-1 when a `}` came after that `{`, or none did).\n * @param value - a raw value\n * @returns the opening index by closing index\n */\nfunction braceBlocks(value: string): Map<number, number> {\n    const blocks = new Map<number, number>();\n    let quoted = false;\n    let open = -1;\n    for (let i = 0; i < value.length; i++) {\n        const ch = value[i];\n        if (ch === \"\\\\\") {\n            i++;\n            continue;\n        }\n        if (ch === '\"') {\n            quoted = !quoted;\n        } else if (!quoted && ch === \"{\") {\n            open = i;\n        } else if (!quoted && ch === \"}\") {\n            blocks.set(i, open);\n            open = -1;\n        }\n    }\n    return blocks;\n}\n\n/**\n * The index of an unescaped `{` outside quotes that no `}` closes: a qualifier block cut short (a\n * file truncated inside it).\n * @param value - a raw value, closing blocks already split off\n * @returns the index, or -1 when every brace is closed\n * @category Plugin helpers\n */\nexport function unclosedBlock(value: string): number {\n    let quoted = false;\n    let open = -1;\n    for (let i = 0; i < value.length; i += value[i] === \"\\\\\" ? 2 : 1) {\n        const ch = value[i];\n        if (ch === \"\\\\\") {\n            continue;\n        }\n        if (ch === '\"' && open < 0) {\n            quoted = !quoted;\n        } else if (!quoted && ch === \"{\") {\n            open = i;\n        } else if (!quoted && ch === \"}\") {\n            open = -1;\n        }\n    }\n    return open;\n}\n\n/**\n * Add one qualifier, turning a repeated name into a list (a list the record owns, appended to in\n * place). The record must have a null prototype, so a name such as `__proto__` is an own key.\n * @param record - the record\n * @param name - the name\n * @param value - the value (or values)\n */\nfunction addQualifier(record: Qualifiers, name: string, value: string | string[]): void {\n    const values = Array.isArray(value) ? value : [value];\n    if (!Object.prototype.hasOwnProperty.call(record, name)) {\n        record[name] = Array.isArray(value) ? [...value] : value;\n        return;\n    }\n    const before = record[name];\n    if (Array.isArray(before)) {\n        for (const v of values) {\n            before.push(v);\n        }\n    } else {\n        record[name] = [before, ...values];\n    }\n}\n\n/**\n * Parse the inside of a qualifier block: `name=\"value\"` pairs separated by commas, the 1.2\n * unquoted form (`source=PMID:1`) and missing spaces accepted. A name is everything up to `=`\n * (qualifier names may be IRIs with colons).\n * @param inner - the text between the braces\n * @returns the qualifiers, or null when the block does not parse (a pair without `=`, an unclosed quote)\n * @category Plugin helpers\n */\nexport function parseQualifiers(inner: string): Qualifiers | null {\n    const out: Qualifiers = Object.create(null) as Qualifiers;\n    let i = 0;\n    const n = inner.length;\n    let any = false;\n    while (i < n) {\n        while (i < n && (inner[i] === \" \" || inner[i] === \"\\t\" || inner[i] === \",\")) {\n            i++;\n        }\n        if (i >= n) {\n            break;\n        }\n        const eq = inner.indexOf(\"=\", i);\n        if (eq < 0) {\n            return null;\n        }\n        const name = unescapeObo(inner.slice(i, eq).trim());\n        if (name.length === 0 || name.includes('\"')) {\n            return null;\n        }\n        i = eq + 1;\n        while (i < n && (inner[i] === \" \" || inner[i] === \"\\t\")) {\n            i++;\n        }\n        let value: string;\n        if (inner[i] === '\"') {\n            const end = closingQuote(inner, i + 1);\n            if (end < 0) {\n                return null;\n            }\n            value = unescapeObo(inner.slice(i + 1, end));\n            i = end + 1;\n        } else {\n            let end = i;\n            while (end < n && inner[end] !== \",\") {\n                end += inner[end] === \"\\\\\" ? 2 : 1;\n            }\n            value = unescapeObo(inner.slice(i, end).trim());\n            i = end;\n        }\n        addQualifier(out, name, value);\n        any = true;\n    }\n    return any ? out : null;\n}\n\n/**\n * The index of the unescaped closing quote.\n * @param text - the text\n * @param from - the index after the opening quote\n * @returns the index, or -1 when the text ends first\n */\nfunction closingQuote(text: string, from: number): number {\n    for (let i = from; i < text.length; i++) {\n        if (text[i] === \"\\\\\") {\n            i++;\n        } else if (text[i] === '\"') {\n            return i;\n        }\n    }\n    return -1;\n}\n\n/**\n * One token of a value.\n * @category Plugin helpers\n */\nexport interface Token {\n    /** A bare word, a quoted string or a bracketed list. */\n    readonly kind: \"word\" | \"quoted\" | \"list\";\n    /** The token's text: unescaped for a word or a quoted string, raw inside the brackets for a list. */\n    readonly text: string;\n    /** Whether the quote or bracket was never closed (the token runs to the end of the value). */\n    readonly unterminated: boolean;\n}\n\n/**\n * Split a value (comment and qualifiers removed) into words, quoted strings and bracketed lists.\n * Whitespace separates tokens; an escaped space belongs to its word.\n * @param value - the raw value\n * @returns the tokens\n * @category Plugin helpers\n */\nexport function tokenize(value: string): Token[] {\n    const tokens: Token[] = [];\n    const n = value.length;\n    let i = 0;\n    while (i < n) {\n        const ch = value[i];\n        if (ch === \" \" || ch === \"\\t\") {\n            i++;\n            continue;\n        }\n        if (ch === '\"') {\n            const end = closingQuote(value, i + 1);\n            const stop = end < 0 ? n : end;\n            // a 1.4 language tag glued to the closing quote (\"chat\"@fr) is kept with the text, as an\n            // unquoted chat@fr is (research-obo.md 4.1: no language is split out)\n            let after = stop + 1;\n            if (end >= 0 && value[after] === \"@\") {\n                while (after < n && value[after] !== \" \" && value[after] !== \"\\t\") {\n                    after++;\n                }\n            }\n            const suffix = end < 0 ? \"\" : value.slice(stop + 1, after);\n            tokens.push({\n                kind: \"quoted\",\n                text: unescapeObo(value.slice(i + 1, stop)) + suffix,\n                unterminated: end < 0,\n            });\n            i = after;\n            continue;\n        }\n        if (ch === \"[\") {\n            const end = closingBracket(value, i + 1);\n            const stop = end < 0 ? n : end;\n            tokens.push({ kind: \"list\", text: value.slice(i + 1, stop), unterminated: end < 0 });\n            i = stop + 1;\n            continue;\n        }\n        let end = i;\n        while (end < n && value[end] !== \" \" && value[end] !== \"\\t\") {\n            end += value[end] === \"\\\\\" ? 2 : 1;\n        }\n        tokens.push({ kind: \"word\", text: unescapeObo(value.slice(i, Math.min(end, n))), unterminated: false });\n        i = end;\n    }\n    return tokens;\n}\n\n/**\n * The index of the unescaped `]` outside quotes closing a list.\n * @param text - the text\n * @param from - the index after `[`\n * @returns the index, or -1 when the text ends first\n */\nfunction closingBracket(text: string, from: number): number {\n    let quoted = false;\n    for (let i = from; i < text.length; i++) {\n        const ch = text[i];\n        if (ch === \"\\\\\") {\n            i++;\n        } else if (ch === '\"') {\n            quoted = !quoted;\n        } else if (ch === \"]\" && !quoted) {\n            return i;\n        }\n    }\n    return -1;\n}\n\n/**\n * One cross-reference: `ID \"description\" {qualifiers}`.\n * @category Plugin helpers\n */\nexport interface Xref {\n    /** The id (may hold spaces: `NIST Chemistry WebBook:110-63-4`, which owlapi reads). */\n    readonly id: string;\n    /** The description, or null. */\n    readonly description: string | null;\n    /** Per-xref qualifiers (OBO 1.2 inside a list), or null. */\n    readonly qualifiers: Qualifiers | null;\n    /** Whether the description's quote was never closed (it runs to the end). */\n    readonly unterminated: boolean;\n}\n\n/**\n * Read one cross-reference: the id is the text before the first unescaped quote, the quoted\n * string its description, a closing block its qualifiers.\n * @param raw - the raw text of one xref\n * @returns the xref, or null when it has no id\n * @category Plugin helpers\n */\nexport function parseXref(raw: string): Xref | null {\n    const { value, qualifiers } = splitQualifiers(raw.trim());\n    let quote = -1;\n    for (let i = 0; i < value.length; i++) {\n        if (value[i] === \"\\\\\") {\n            i++;\n        } else if (value[i] === '\"') {\n            quote = i;\n            break;\n        }\n    }\n    const id = unescapeObo((quote < 0 ? value : value.slice(0, quote)).trim());\n    if (id.length === 0) {\n        return null;\n    }\n    let description: string | null = null;\n    let unterminated = false;\n    if (quote >= 0) {\n        const end = closingQuote(value, quote + 1);\n        unterminated = end < 0;\n        description = unescapeObo(value.slice(quote + 1, end < 0 ? value.length : end));\n    }\n    return { id, description, qualifiers, unterminated };\n}\n\n/**\n * Split the inside of a bracketed list into xrefs at the unescaped commas outside quotes and\n * braces (a solitary xref needs no escaping of its commas only outside a list).\n * @param inner - the raw text between the brackets\n * @returns the xrefs, in order\n * @category Plugin helpers\n */\nexport function parseXrefList(inner: string): Xref[] {\n    const out: Xref[] = [];\n    let quoted = false;\n    let depth = 0;\n    let start = 0;\n    const flush = (end: number): void => {\n        const xref = parseXref(inner.slice(start, end));\n        if (xref !== null) {\n            out.push(xref);\n        }\n    };\n    for (let i = 0; i < inner.length; i++) {\n        const ch = inner[i];\n        if (ch === \"\\\\\") {\n            i++;\n        } else if (ch === '\"') {\n            quoted = !quoted;\n        } else if (!quoted && ch === \"{\") {\n            depth++;\n        } else if (!quoted && ch === \"}\") {\n            depth = Math.max(0, depth - 1);\n        } else if (!quoted && depth === 0 && ch === \",\") {\n            flush(i);\n            start = i + 1;\n        }\n    }\n    flush(inner.length);\n    return out;\n}\n\n/**\n * Whether the raw value holds an unescaped `{` or `}` outside quotes and outside a bracketed xref\n * list (a brace mid-value that is not a closing qualifier block is literal text the writer should\n * have escaped).\n * @param value - the raw value, qualifiers already split off\n * @returns true when a stray brace is present\n * @category Plugin helpers\n */\nexport function hasStrayBrace(value: string): boolean {\n    let quoted = false;\n    let listed = false;\n    for (let i = 0; i < value.length; i++) {\n        const ch = value[i];\n        if (ch === \"\\\\\") {\n            i++;\n        } else if (ch === '\"') {\n            quoted = !quoted;\n        } else if (!quoted && (ch === \"[\" || ch === \"]\")) {\n            // inside an xref list a brace opens that xref's qualifiers (OBO 1.2)\n            listed = ch === \"[\";\n        } else if (!quoted && !listed && (ch === \"{\" || ch === \"}\")) {\n            return true;\n        }\n    }\n    return false;\n}\n\n// ============================================================ the writer side\n\n/** A carriage return, a CRLF pair or a form feed: line ends OBO text cannot carry. */\nconst LINE_ENDS = /\\r\\n|\\r|\\f/g;\n\n/**\n * Whether a text holds a carriage return or a form feed, which the OBO line grammar reads as a line\n * end wherever it stands and no escape can spell; the writers turn them into `\\n`.\n * @param text - the text\n * @returns true when the text loses a character on the way through an OBO file\n * @category Plugin helpers\n */\nexport function hasLineEnd(text: string): boolean {\n    return text.includes(\"\\r\") || text.includes(\"\\f\");\n}\n\n/**\n * Escape text for a quoted OBO string (`def: \"...\"`, a synonym, a qualifier value): backslash,\n * quote, newline and tab. A carriage return or form feed becomes a newline (see hasLineEnd()).\n * `\\W` is never written: graph-io reads it as a space, fastobo and the 1.4 BNF as the letter W.\n * @param text - the text\n * @returns the escaped text, without the quotes\n * @category Plugin helpers\n */\nexport function escapeOboQuoted(text: string): string {\n    return text.replaceAll(LINE_ENDS, \"\\n\").replaceAll(/[\\\\\"\\n\\t]/g, (ch) => {\n        switch (ch) {\n            case \"\\n\":\n                return String.raw`\\n`;\n            case \"\\t\":\n                return String.raw`\\t`;\n            default:\n                return `\\\\${ch}`;\n        }\n    });\n}\n\n/**\n * Escape text for an unquoted OBO value (`name:`, `comment:`, an xref id, an unknown tag): what\n * escapeOboQuoted() escapes plus `!` (a comment), `{` and `}` (a qualifier block), `[`, `]` and `,`\n * (an xref list) and `\"` (a quoted string). The reader trims an unquoted value, so its leading\n * and trailing spaces cannot be kept.\n * @param text - the text\n * @returns the escaped text\n * @category Plugin helpers\n */\nexport function escapeOboValue(text: string): string {\n    return escapeOboQuoted(text).replaceAll(/[!{}[\\],]/g, (ch) => `\\\\${ch}`);\n}\n\n/**\n * Whether a text can stand as one OBO word (an id, a relation, a subset or synonym type name): not\n * empty, no whitespace, no control character (the importer refuses an id holding one), no `!`, `{`\n * or `}`. escapeOboWord() escapes what else would end it or turn\n * it into another token (a backslash, a quote, a leading `[`).\n * @param text - the text\n * @returns true when the text is a word\n * @category Plugin helpers\n */\nexport function isOboWord(text: string): boolean {\n    return text.length > 0 && !NOT_IN_WORD.test(text);\n}\n\n/**\n * A character an OBO word cannot hold: whitespace, a control character, `!`, `{` or `}`.\n * @category Plugin helpers\n */\nexport const NOT_IN_WORD = /[\\s!{}\\p{Cc}]/u;\n\n/**\n * Write a word (see isOboWord()): a backslash and a quote escaped, and a leading `[` (which would\n * open an xref list).\n * @param word - a text isOboWord() accepts\n * @returns the text to write\n * @category Plugin helpers\n */\nexport function escapeOboWord(word: string): string {\n    const out = word.replaceAll(/[\\\\\"]/g, (ch) => `\\\\${ch}`);\n    return out.startsWith(\"[\") ? `\\\\${out}` : out;\n}\n\n/**\n * Whether a text can be a qualifier name: not empty, no surrounding space, none of `=`, `\"`, `,`,\n * `{`, `}`, `[`, `]`, `!`, a backslash or a line end (the reader takes a name as everything up to\n * the first `=`, unescaped only after the split).\n * @param name - the name\n * @returns true when the name is written as it is\n * @category Plugin helpers\n */\nexport function isQualifierName(name: string): boolean {\n    return name.length > 0 && name === name.trim() && !/[=\",{}[\\]!\\\\\\n\\r\\t\\f]/.test(name);\n}\n\n/**\n * A qualifier block: `{name=\"value\", ...}`, a list value as one pair per item.\n * @param pairs - the name / value pairs, in order (names isQualifierName() accepts)\n * @returns the block with a leading space, or \"\" when there are no pairs\n * @category Plugin helpers\n */\nexport function qualifierBlock(pairs: readonly (readonly [string, string])[]): string {\n    if (pairs.length === 0) {\n        return \"\";\n    }\n    const items = pairs.map(([name, value]) => `${name}=\"${escapeOboQuoted(value)}\"`);\n    return ` {${items.join(\", \")}}`;\n}\n","/**\n * The OBO importer (design section 4; research-obo.md): the line-oriented OBO flat file format of\n * the Gene Ontology and the OBO Foundry, versions 1.0, 1.2 and 1.4 read as their union (real files\n * do not say which they follow: the GO writes `format-version: 1.2` and uses 1.4 tags), streamed\n * through the common LineReader.\n *\n * `[Term]` and `[Instance]` frames are nodes; `is_a`, `relationship` and `instance_of` clauses are\n * directed edges from the frame to the target, with the relation in a `relation` dict column (role\n * `kind`) and the trailing qualifier block in a `qualifiers` json column. `[Typedef]` frames are\n * metadata (`meta.extra.obo.typedefs`) unless `typedefs: \"nodes\"`. Every other tag fills the\n * column of its name (src/common/ontology.ts); an unknown tag is kept in `obo.unrecognized`.\n * Frames that share an id are merged (spec 4.1.1): list clauses take the union, a single-valued\n * clause keeps the first. A target no frame declares becomes a placeholder node (the guide's\n * recommended reading; ontologies point into their imports this way) unless `addMissingNodes` is\n * false.\n *\n * ponytail: the frames are held until the end of the file (merging needs every frame of an id,\n * dangling detection the whole id set), so memory is about twice the snapshot's; a two-pass reader\n * would lift that for files beyond a few hundred megabytes.\n */\n\nimport {\n    type ColumnHandle,\n    GraphFormatError,\n    type GraphMetaPatch,\n    type GraphSink,\n    INVALID_INDEX,\n    type NodeId,\n} from \"@graphty/graph-format\";\n\nimport { declareResolved, RENAMED_CODE, ROLE_TAKEN_CODE } from \"../../common/attributes.js\";\nimport {\n    BAD_VALUE_CODE,\n    DANGLING_REFERENCE_CODE,\n    DUPLICATE_ATTRIBUTE_CODE,\n    DUPLICATE_NODE_CODE,\n    ELEMENT_ISSUE,\n    EMPTY_INPUT_CODE,\n    ENCODING_FALLBACK_CODE,\n    INPUT_ISSUE,\n    INVALID_ENCODING_CODE,\n    INVALID_UTF8_CODE,\n    MISSING_ID_CODE,\n    OPTION_IGNORED_CODE,\n    UNKNOWN_ELEMENT_CODE,\n    UNKNOWN_ENCODING_CODE,\n} from \"../../common/codes.js\";\nimport { DirectionResolver } from \"../../common/direction.js\";\nimport { ID_MERGED_CODE, IdCoercer } from \"../../common/ids.js\";\nimport { LineReader, throwIfAborted } from \"../../common/input.js\";\nimport { OBO_NODE_COLUMNS, oboColumnDecl, PLACEHOLDER_COLUMN, SYNONYM_SCOPES } from \"../../common/ontology.js\";\nimport {\n    type ImportFormatDefaults,\n    reportSinkOptions,\n    reportUnusedOptions,\n    resolveImportOptions,\n    SINK_OPTION_CODE,\n} from \"../../common/options.js\";\nimport { agree, plural } from \"../../common/plural.js\";\nimport { ImportReportBuilder } from \"../../common/report.js\";\nimport { type CommonImportOptions, type GraphImporter, type ImportInput, type ImportReport } from \"../../types.js\";\nimport {\n    endsWithContinuation,\n    hasStrayBrace,\n    parseXref,\n    parseXrefList,\n    type Qualifiers,\n    splitFormFeeds,\n    splitQualifiers,\n    splitTagValue,\n    stripComment,\n    type Token,\n    tokenize,\n    unclosedBlock,\n    unescapeObo,\n    type Xref,\n} from \"./syntax.js\";\n\n/**\n * The format-specific options of the OBO importer.\n * @category Built-in formats\n */\nexport interface OboImportOptions extends CommonImportOptions {\n    /**\n     * \"keep\" reads obsolete terms as nodes with `is_obsolete` set to true; \"drop\" leaves them and\n     * their edges out.\n     * @defaultValue \"keep\"\n     */\n    obsolete?: \"keep\" | \"drop\" | undefined;\n    /**\n     * \"metadata\" keeps the `[Typedef]` frames (relation definitions) in\n     * `snapshot.meta.extra.obo.typedefs`; \"nodes\" makes them nodes too, with their `is_a` edges.\n     * @defaultValue \"metadata\"\n     */\n    typedefs?: \"metadata\" | \"nodes\" | undefined;\n}\n\n/**\n * Issue codes of the OBO importer.\n * @category Built-in formats\n */\nexport const OBO_ISSUE = Object.freeze({\n    ...INPUT_ISSUE,\n    ...ELEMENT_ISSUE,\n    /** The input is empty or whitespace. The import stops. */\n    EMPTY_INPUT: EMPTY_INPUT_CODE,\n    /** The input is not valid UTF-8. The import stops. */\n    INVALID_UTF8: INVALID_UTF8_CODE,\n    /**\n     * Some bytes are not valid in the encoding that was chosen (by a byte order mark or the `encoding` option). The\n     * import stops.\n     */\n    INVALID_ENCODING: INVALID_ENCODING_CODE,\n    /** Bytes that are not UTF-8 were read as windows-1252. */\n    ENCODING_FALLBACK: ENCODING_FALLBACK_CODE,\n    /** A declared encoding the platform cannot decode was ignored. */\n    UNKNOWN_ENCODING: UNKNOWN_ENCODING_CODE,\n    /** A frame without an `id` clause; the frame is skipped. */\n    MISSING_ID: MISSING_ID_CODE,\n    /** A clause whose value cannot be read (a boolean other than true / false, a relationship with one or three values); the clause is skipped. */\n    BAD_VALUE: BAD_VALUE_CODE,\n    /** Two frames have the same id, so they were merged into one node. */\n    DUPLICATE_NODE: DUPLICATE_NODE_CODE,\n    /** A tag that may appear once per frame appears twice; the first value is kept. */\n    DUPLICATE_ATTRIBUTE: DUPLICATE_ATTRIBUTE_CODE,\n    /** An unknown tag (kept in `obo.unrecognized`) or frame type (skipped), once per name. */\n    UNKNOWN_ELEMENT: UNKNOWN_ELEMENT_CODE,\n    /** A target no frame declares: a placeholder node was made, or the edge dropped under addMissingNodes false. */\n    DANGLING_REFERENCE: DANGLING_REFERENCE_CODE,\n    /** A line without a colon, an unterminated quote, a def without its xref list, a qualifier block that does not parse, an unescaped brace. */\n    SYNTAX: \"W_OBO_SYNTAX\",\n    /**\n     * Nothing in the input looks like OBO: there is no frame header and no header tag. It may be an HTML page, a JSON\n     * or GML file, or UTF-16 text without a byte order mark. The import stops.\n     */\n    NOT_OBO: \"E_OBO_NOT_OBO\",\n    /**\n     * The header has no `format-version` (OBO 1.2 and 1.4 require one), or names a version other than 1.0, 1.2 or 1.4.\n     * The file is read accepting the tags of every version.\n     */\n    FORMAT_VERSION: \"W_OBO_FORMAT_VERSION\",\n    /** The frame's `id` is not its first clause; it is used anyway. */\n    ID_NOT_FIRST: \"W_OBO_ID_NOT_FIRST\",\n    /** A synonym without a scope in a file that does not say 1.2, or with a scope that is not one of the four. */\n    SYNONYM_SCOPE: \"W_OBO_SYNONYM_SCOPE\",\n    /** A relation, subset or synonym type that nothing declares. */\n    UNDECLARED: \"W_OBO_UNDECLARED\",\n    /** One id for a Term and a Typedef (or an Instance); the Term (the first node frame) is the node. */\n    ID_KIND_CLASH: \"W_OBO_ID_KIND_CLASH\",\n    /** A frame has only one `intersection_of` or `union_of` clause, where OBO needs at least two. */\n    CARDINALITY: \"W_OBO_CARDINALITY\",\n    /** An obsolete term with is_a / relationship, or replaced_by / consider on a term that is not obsolete. */\n    OBSOLETION: \"W_OBO_OBSOLETION\",\n    /** An OBO 1.0 / 1.2 tag read as its 1.4 meaning (exact_synonym, xref_analog, use_term, typeref, version). */\n    DEPRECATED_TAG: \"W_OBO_DEPRECATED_TAG\",\n    /** A backslash line continuation (deprecated in 1.4). */\n    DEPRECATED_SYNTAX: \"W_OBO_DEPRECATED_SYNTAX\",\n    /**\n     * A header clause whose meaning graph-io does not apply (`import`, `id-mapping`, the `treat-xrefs` macros,\n     * `owl-axioms`); it is kept in `snapshot.meta.extra.obo.header`.\n     */\n    HEADER_NOT_APPLIED: \"W_OBO_HEADER_NOT_APPLIED\",\n    /** Obsolete terms and their edges left out under obsolete: \"drop\". */\n    OBSOLETE_DROPPED: \"W_OBO_OBSOLETE_DROPPED\",\n    /**\n     * Two different id texts became the same number because `ids` is \"number\" (for example, \"042\" and \"42\"), so their nodes\n     * were merged.\n     */\n    ID_MERGED: ID_MERGED_CODE,\n    /** An OBO attribute was renamed `<name>#obo` because another attribute already has its name. */\n    COLUMN_RENAMED: RENAMED_CODE,\n    /**\n     * You read into a graph builder that already has an id, label or position attribute, so this file's one is kept as\n     * a plain attribute.\n     */\n    ROLE_TAKEN: ROLE_TAKEN_CODE,\n    /** You set an option this format does not use; it had no effect. The message names the option. */\n    OPTION_IGNORED: OPTION_IGNORED_CODE,\n    /**\n     * You read into your own graph builder, which was created with a different `addMissingNodes`, `duplicateEdges`,\n     * `selfLoops` or `weightDtype` than the option you passed; the builder's setting applies.\n     */\n    SINK_OPTION: SINK_OPTION_CODE,\n});\n\n/** The common options the OBO importer reads. */\nconst USED_OPTIONS: ReadonlySet<keyof CommonImportOptions> = new Set<keyof CommonImportOptions>([\n    \"ids\",\n    \"addMissingNodes\",\n    \"duplicateEdges\",\n    \"selfLoops\",\n    \"onMixedDirection\",\n    \"weightDtype\",\n    \"errorLimit\",\n    \"signal\",\n    \"onProgress\",\n    \"encoding\",\n    \"restoreMangledIds\",\n]);\n\n/** The property_value relation under which the exporter keeps an id it rewrote (`sanitizeIds: \"mangle\"`). */\nconst ORIGINAL_ID = \"graphty:originalId\";\n\nconst DEFAULTS: ImportFormatDefaults = { ids: \"keep\", defaultDirected: true, weightFrom: null };\n\n/** Frames between two checks of the cancellation signal. */\nconst ABORT_CHECK_INTERVAL = 64;\n\n/** Bytes of the head sniff() reads. */\nconst SNIFF_BYTES = 4096;\n\nconst FRAME_KINDS: ReadonlySet<string> = new Set([\"Term\", \"Typedef\", \"Instance\"]);\n\n/** Header tags kept but not applied (design 4.3, W_OBO_HEADER_NOT_APPLIED). */\nconst NOT_APPLIED_HEADER = /^(import|typeref|id-mapping|default-relationship-id-prefix|owl-axioms|treat-xrefs-as-.*)$/;\n\n/** Deprecated header tags and what they are now. */\nconst DEPRECATED_HEADER: ReadonlyMap<string, string> = new Map([\n    [\"typeref\", \"import\"],\n    [\"version\", \"data-version\"],\n]);\n\n/**\n * The 1.0 / 1.2 frame tags read as their 1.4 meaning: tag to [1.4 tag, synonym scope].\n * @category Plugin helpers\n */\nexport const DEPRECATED_TAGS: ReadonlyMap<string, readonly [string, string | null]> = new Map([\n    [\"exact_synonym\", [\"synonym\", \"EXACT\"]],\n    [\"narrow_synonym\", [\"synonym\", \"NARROW\"]],\n    [\"broad_synonym\", [\"synonym\", \"BROAD\"]],\n    [\"related_synonym\", [\"synonym\", \"RELATED\"]],\n    [\"xref_analog\", [\"xref\", null]],\n    [\"xref_unk\", [\"xref\", null]],\n    [\"xref_unknown\", [\"xref\", null]],\n    [\"use_term\", [\"consider\", null]],\n]);\n\n/** Relations every OBO file may use without a Typedef (the 1.2 built-ins). */\nconst BUILTIN_RELATIONS: ReadonlySet<string> = new Set([\n    \"is_a\",\n    \"instance_of\",\n    \"disjoint_from\",\n    \"inverse_of\",\n    \"union_of\",\n    \"intersection_of\",\n]);\n\n/**\n * Single-valued text tags (first value kept).\n * @category Plugin helpers\n */\nexport const TEXT_TAGS: ReadonlySet<string> = new Set([\n    \"name\",\n    \"namespace\",\n    \"comment\",\n    \"created_by\",\n    \"creation_date\",\n    \"domain\",\n    \"range\",\n    \"inverse_of\",\n]);\n\n/**\n * Single-valued boolean tags.\n * @category Plugin helpers\n */\nexport const BOOL_TAGS: ReadonlySet<string> = new Set(\n    Object.keys(OBO_NODE_COLUMNS).filter((name) => OBO_NODE_COLUMNS[name].dtype === \"bool\"),\n);\n\n/**\n * Tags whose value is one id, collected in a list column.\n * @category Plugin helpers\n */\nexport const ID_LIST_TAGS: ReadonlySet<string> = new Set([\n    \"alt_id\",\n    \"subset\",\n    \"replaced_by\",\n    \"consider\",\n    \"union_of\",\n    \"equivalent_to\",\n    \"disjoint_from\",\n    \"transitive_over\",\n    \"disjoint_over\",\n]);\n\n/** Header tags the specification allows once (the first is kept). */\nconst SINGLE_HEADER_TAGS: ReadonlySet<string> = new Set([\n    \"format-version\",\n    \"data-version\",\n    \"version\",\n    \"date\",\n    \"saved-by\",\n    \"auto-generated-by\",\n    \"default-namespace\",\n    \"ontology\",\n    \"default-relationship-id-prefix\",\n]);\n\n/** The format versions the importer knows (it reads their union). */\nconst KNOWN_VERSION = /^(GO_)?1\\.[024]$/;\n\n/** Tags whose value is an id, where a qualifier block cut short by a truncated file is dropped. */\nconst ID_VALUE_TAGS: ReadonlySet<string> = new Set([\n    ...ID_LIST_TAGS,\n    \"is_a\",\n    \"instance_of\",\n    \"relationship\",\n    \"intersection_of\",\n]);\n\n/** Warnings listed per code before the rest are summed up in one (a file of 50k unknown tags). */\nconst MAX_TALLIES_PER_CODE = 100;\n\n/**\n * Whether a text holds a control character other than tab, line feed, form feed (a line end in\n * the 1.4 grammar, text inside quotes) and carriage return.\n * @param text - the text\n * @returns true when it does\n */\nfunction hasControl(text: string): boolean {\n    for (const ch of text) {\n        if ((ch < \" \" && ch !== \"\\t\" && ch !== \"\\n\" && ch !== \"\\f\" && ch !== \"\\r\") || ch === \"\\x7f\") {\n            return true;\n        }\n    }\n    return false;\n}\n\n/**\n * Whether a tag could name an OBO tag: no whitespace, control characters or the punctuation of\n * other formats (`{`, `\"`, `<`, brackets, parentheses).\n * @param tag - the tag\n * @returns true for a plausible tag\n */\nfunction isTagName(tag: string): boolean {\n    return tag.length > 0 && !hasControl(tag) && !/[\\s{}\"<>[\\]()]/.test(tag);\n}\n\n/**\n * A record with no prototype, so a key named after an Object.prototype member (`__proto__`,\n * `constructor`, `toString`) is an own key like any other.\n * @returns the empty record\n */\nfunction ownRecord<T>(): Record<string, T> {\n    return Object.create(null) as Record<string, T>;\n}\n\n/**\n * Append a value to the list of a key in a null-prototype record.\n * @param map - the record\n * @param key - the key\n * @param value - the value\n */\nfunction append<T>(map: Record<string, T[]>, key: string, value: T): void {\n    if (Object.hasOwn(map, key)) {\n        map[key].push(value);\n    } else {\n        map[key] = [value];\n    }\n}\n\n/**\n * Tags that only a Typedef frame may carry (elsewhere they are unrecognized).\n * @category Plugin helpers\n */\nexport const TYPEDEF_TAGS: ReadonlySet<string> = new Set([\n    \"domain\",\n    \"range\",\n    \"inverse_of\",\n    \"transitive_over\",\n    \"disjoint_over\",\n    \"holds_over_chain\",\n    \"equivalent_to_chain\",\n    \"expand_assertion_to\",\n    \"expand_expression_to\",\n    \"is_cyclic\",\n    \"is_reflexive\",\n    \"is_symmetric\",\n    \"is_anti_symmetric\",\n    \"is_asymmetric\",\n    \"is_transitive\",\n    \"is_functional\",\n    \"is_inverse_functional\",\n    \"is_metadata_tag\",\n    \"is_class_level\",\n]);\n\ntype FrameKind = \"Term\" | \"Typedef\" | \"Instance\";\n\n/** One clause as read: the tag and the raw value without its comment. */\ninterface Clause {\n    readonly tag: string;\n    readonly value: string;\n    readonly line: number;\n}\n\n/** An edge held until the end of the file. */\ninterface PendingEdge {\n    readonly relation: string;\n    readonly target: string;\n    readonly qualifiers: Qualifiers | null;\n    readonly line: number;\n}\n\n/** Everything read for one id, over all of its frames. */\ninterface NodeRecord {\n    readonly id: string;\n    readonly kind: FrameKind;\n    readonly line: number;\n    /** Single values and whole-cell values by column. */\n    readonly values: Map<string, unknown>;\n    /** List and json-list cells by column. */\n    readonly lists: Map<string, unknown[]>;\n    readonly edges: PendingEdge[];\n    /** The clauses already applied (spec 4.1.1: an identical clause counts once). */\n    readonly seen: Set<string>;\n    /** Typedef frames: every clause by tag, raw, for `meta.extra.obo.typedefs`. */\n    readonly raw: Record<string, string[]>;\n}\n\n/** Where a clause is: its line and the id of its frame. */\ninterface Where {\n    readonly line: number;\n    readonly element: string;\n}\n\n/** A warning counted while reading and recorded once at the end. */\ninterface Tally {\n    readonly category: \"parse-error\" | \"validation-error\" | \"coercion\" | \"unsupported\" | \"merged\";\n    readonly code: string;\n    readonly element: string;\n    readonly what: string;\n    readonly line: number;\n    count: number;\n}\n\n/** The OBO-specific options, resolved. */\ninterface ResolvedOboOptions {\n    readonly obsolete: \"keep\" | \"drop\";\n    readonly typedefs: \"metadata\" | \"nodes\";\n}\n\n/**\n * Resolve the OBO-specific options.\n * @param options - the caller's options\n * @returns the resolved options; E_UNSUPPORTED for a value outside its set\n */\nfunction resolveOboOptions(options: OboImportOptions | undefined): ResolvedOboOptions {\n    const obsolete = options?.obsolete ?? \"keep\";\n    const typedefs = options?.typedefs ?? \"metadata\";\n    if (obsolete !== \"keep\" && obsolete !== \"drop\") {\n        throw unsupported(\"obsolete\", obsolete, [\"keep\", \"drop\"]);\n    }\n    if (typedefs !== \"metadata\" && typedefs !== \"nodes\") {\n        throw unsupported(\"typedefs\", typedefs, [\"metadata\", \"nodes\"]);\n    }\n    return { obsolete, typedefs };\n}\n\n/**\n * The E_UNSUPPORTED error of an option outside its set.\n * @param option - the option name\n * @param found - the value\n * @param supported - the allowed values\n * @returns the error\n */\nfunction unsupported(option: string, found: unknown, supported: readonly string[]): Error {\n    return new GraphFormatError(\n        \"E_UNSUPPORTED\",\n        `option ${option}: ${JSON.stringify(found)} is not one of ${supported.join(\", \")}`,\n        {\n            option,\n            found,\n            supported,\n        },\n    );\n}\n\n/** One import's state. */\nclass OboReader {\n    private readonly report: ImportReportBuilder;\n\n    private readonly signal: AbortSignal | null;\n\n    /** Header clauses by tag, raw, in order. */\n    private readonly header: Record<string, string[]> = ownRecord<string[]>();\n\n    /** Whether `[Typedef]` frames are nodes (typedefs \"nodes\"). */\n    private readonly typedefsAsNodes: boolean;\n\n    /** Whether any frame header was read. */\n    private frameSeen = false;\n\n    /** Header clauses whose tag could be an OBO tag. */\n    private tagClauses = 0;\n\n    /** The first line that is not a frame header, a comment or a tag-value line with a plausible tag. */\n    private firstBadLine: number | null = null;\n\n    private version: string | null = null;\n\n    private defaultNamespace: string | null = null;\n\n    private readonly subsets = new Set<string>();\n\n    /** Declared synonym types and their default scope (null: none). */\n    private readonly synonymTypes = new Map<string, string | null>();\n\n    /** Node frames (Term, Instance) by id, in first-appearance order. */\n    readonly nodes = new Map<string, NodeRecord>();\n\n    /** Typedef frames by id. */\n    readonly typedefs = new Map<string, NodeRecord>();\n\n    private readonly tallies = new Map<string, Tally>();\n\n    /** The frame being read: its kind (null for an unknown frame type), name and clauses. */\n    private frame: { kind: FrameKind | null; name: string; line: number; clauses: Clause[] } | null = null;\n\n    /** The frames of an unknown type, raw, for `meta.extra.obo.unknownFrames`. */\n    readonly unknownFrames: { type: string; clauses: Record<string, string[]> }[] = [];\n\n    private framesSinceCheck = 0;\n\n    /** Whether any significant line was read. */\n    significant = false;\n\n    /**\n     * Create a reader.\n     * @param report - the report\n     * @param signal - the cancellation signal\n     * @param typedefsAsNodes - whether `[Typedef]` frames are nodes\n     */\n    constructor(report: ImportReportBuilder, signal: AbortSignal | null, typedefsAsNodes: boolean) {\n        this.report = report;\n        this.signal = signal;\n        this.typedefsAsNodes = typedefsAsNodes;\n    }\n\n    /**\n     * Read one logical line.\n     * @param text - the line, continuation joined\n     * @param line - its 1-based number\n     */\n    line(text: string, line: number): void {\n        const t = text.trim();\n        if (t.length === 0) {\n            return;\n        }\n        this.significant = true;\n        if (t.startsWith(\"!\")) {\n            return;\n        }\n        if (t.startsWith(\"[\") && this.frameHeader(t, line)) {\n            return;\n        }\n        // the comment goes first, so a colon inside it never makes `foo ! a:b` a tag-value line\n        const tv = splitTagValue(stripComment(t));\n        if (tv === null || tv.tag.length === 0) {\n            this.firstBadLine ??= line;\n            const what = tv === null ? \"a line without a colon was skipped\" : \"a line without a tag was skipped\";\n            this.tally(\"parse-error\", OBO_ISSUE.SYNTAX, what, \"line\", line);\n            return;\n        }\n        const clause: Clause = { tag: tv.tag, value: stripComment(tv.rest), line };\n        if (this.frame === null) {\n            if (isTagName(tv.tag)) {\n                this.tagClauses++;\n            } else {\n                this.firstBadLine ??= line;\n            }\n            this.headerClause(clause);\n        } else {\n            this.frame.clauses.push(clause);\n        }\n    }\n\n    /**\n     * Start a frame at a line opening with `[`: a well-formed header, or one damaged so that only a\n     * frame header can be meant (a known frame name, or no colon: `[Term`, `[Term] extra`), with a\n     * warning, so the clauses after it never merge into the frame before.\n     * @param t - the trimmed line\n     * @param line - its number\n     * @returns false when the line is not a frame header\n     */\n    private frameHeader(t: string, line: number): boolean {\n        const close = t.indexOf(\"]\");\n        const name = (close < 0 ? t.slice(1) : t.slice(1, close)).trim();\n        const after = close < 0 ? \"\" : t.slice(close + 1).trim();\n        const clean = close >= 0 && (after.length === 0 || after.startsWith(\"!\"));\n        if (!clean && !FRAME_KINDS.has(name) && t.includes(\":\")) {\n            return false;\n        }\n        if (!clean) {\n            const what =\n                close < 0\n                    ? \"a frame header without its closing ] starts the frame\"\n                    : \"text after a frame header was ignored\";\n            this.tally(\"parse-error\", OBO_ISSUE.SYNTAX, what, `[${name}]`, line);\n        }\n        // a known frame name, or a clean header with a name: anything else (`[`, `[{\"id\": 1}]`, a JSON\n        // array) is read as a damaged header but is no proof the input is OBO\n        const proof = FRAME_KINDS.has(name) || (clean && /^[A-Za-z]/.test(name) && isTagName(name));\n        if (!proof) {\n            this.firstBadLine ??= line;\n        }\n        this.startFrame(name, line, proof);\n        return true;\n    }\n\n    /**\n     * Start a frame, finishing the one before.\n     * @param name - the frame type\n     * @param line - the header's line\n     * @param proof - whether the header shows the input is OBO\n     */\n    private startFrame(name: string, line: number, proof: boolean): void {\n        this.finishFrame();\n        this.frameSeen ||= proof;\n        const kind = FRAME_KINDS.has(name) ? (name as FrameKind) : null;\n        if (kind === null) {\n            this.tally(\n                \"validation-error\",\n                OBO_ISSUE.UNKNOWN_ELEMENT,\n                \"frames of an unknown type are not nodes; kept in meta.extra.obo.unknownFrames\",\n                `[${name}]`,\n                line,\n            );\n        }\n        this.frame = { kind, name, line, clauses: [] };\n    }\n\n    /**\n     * Record one header clause.\n     * @param clause - the clause\n     */\n    private headerClause(clause: Clause): void {\n        append(this.header, clause.tag, clause.value);\n        const { tag } = clause;\n        if (SINGLE_HEADER_TAGS.has(tag) && this.header[tag].length > 1) {\n            this.tally(\n                \"validation-error\",\n                OBO_ISSUE.DUPLICATE_ATTRIBUTE,\n                \"a single-valued header tag given twice; the first is kept\",\n                tag,\n                clause.line,\n            );\n        }\n        const tokens = tokenize(splitQualifiers(clause.value).value);\n        const first = tokens.length > 0 && tokens[0].kind === \"word\" ? tokens[0].text : null;\n        if (tag === \"format-version\") {\n            this.version ??= unescapeObo(clause.value).trim();\n        } else if (tag === \"default-namespace\") {\n            this.defaultNamespace ??= first;\n        } else if ((tag === \"subsetdef\" || tag === \"synonymtypedef\") && first === null) {\n            this.tally(\n                \"parse-error\",\n                OBO_ISSUE.SYNTAX,\n                \"a declaration whose name is not a word declares nothing\",\n                tag,\n                clause.line,\n            );\n        } else if (tag === \"subsetdef\" && first !== null) {\n            this.subsets.add(first);\n        } else if (tag === \"synonymtypedef\" && first !== null) {\n            const scope = tokens.slice(1).find((t) => t.kind === \"word\" && SYNONYM_SCOPES.has(t.text));\n            this.synonymTypes.set(first, scope?.text ?? null);\n        }\n        const now = DEPRECATED_HEADER.get(tag);\n        if (now !== undefined) {\n            this.tally(\"coercion\", OBO_ISSUE.DEPRECATED_TAG, `the 1.0 header tag is read as ${now}`, tag, clause.line);\n        }\n        if (NOT_APPLIED_HEADER.test(tag)) {\n            this.tally(\n                \"unsupported\",\n                OBO_ISSUE.HEADER_NOT_APPLIED,\n                \"kept in meta.extra.obo.header, not applied\",\n                tag,\n                clause.line,\n            );\n        }\n    }\n\n    /** Finish the frame being read: find its id and merge its clauses into the record of that id. */\n    finishFrame(): void {\n        const { frame } = this;\n        this.frame = null;\n        if (frame === null) {\n            return;\n        }\n        if (frame.kind === null) {\n            // the guides: an unrecognized frame must survive, so its clauses are kept, raw\n            const clauses = ownRecord<string[]>();\n            for (const clause of frame.clauses) {\n                append(clauses, clause.tag, clause.value);\n            }\n            this.unknownFrames.push({ type: frame.name, clauses });\n            return;\n        }\n        if (++this.framesSinceCheck >= ABORT_CHECK_INTERVAL) {\n            this.framesSinceCheck = 0;\n            throwIfAborted(this.signal);\n        }\n        const idAt = frame.clauses.findIndex((c) => c.tag === \"id\");\n        const idParts = idAt < 0 ? null : splitQualifiers(frame.clauses[idAt].value);\n        const rawId = idParts === null ? \"\" : idParts.value.trim();\n        const id = unescapeObo(rawId).trim();\n        // a Typedef is metadata unless typedefs \"nodes\": it would never have been a node\n        const wouldBeNode = frame.kind !== \"Typedef\" || this.typedefsAsNodes;\n        if (id.length === 0) {\n            this.report.error(\n                \"missing-value\",\n                OBO_ISSUE.MISSING_ID,\n                `a [${frame.kind}] frame has no id; it is skipped`,\n                {\n                    line: frame.line,\n                },\n            );\n            if (wouldBeNode) {\n                this.report.counts.skippedNodes++;\n            }\n            return;\n        }\n        if (tokenize(rawId).length > 1 || hasControl(id)) {\n            // a reference cannot name such an id (is_a needs one word), so the frame is refused\n            // rather than made a node no edge can reach\n            this.report.error(\n                \"validation-error\",\n                OBO_ISSUE.BAD_VALUE,\n                `a [${frame.kind}] frame's id ${JSON.stringify(id)} holds unescaped whitespace or a control character; the frame is skipped`,\n                { line: frame.clauses[idAt].line, element: id },\n            );\n            if (wouldBeNode) {\n                this.report.counts.skippedNodes++;\n            }\n            return;\n        }\n        if (idAt > 0) {\n            this.tally(\n                \"validation-error\",\n                OBO_ISSUE.ID_NOT_FIRST,\n                \"the id clause is not the frame's first; it is used\",\n                \"id\",\n                frame.clauses[idAt].line,\n            );\n        }\n        const target = this.recordFor(frame.kind, id, frame.line);\n        this.extraQualifiers(target, \"id\", id, idParts?.qualifiers ?? null);\n        for (let i = 0; i < frame.clauses.length; i++) {\n            const clause = frame.clauses[i];\n            if (clause.tag === \"id\") {\n                if (i !== idAt) {\n                    this.tally(\n                        \"validation-error\",\n                        OBO_ISSUE.DUPLICATE_ATTRIBUTE,\n                        \"a frame names a second id; the first is kept\",\n                        \"id\",\n                        clause.line,\n                    );\n                }\n                continue;\n            }\n            this.applyClause(target, clause);\n        }\n        if (target.kind === \"Typedef\" && !Object.hasOwn(target.raw, \"id\")) {\n            target.raw.id = [id];\n        }\n    }\n\n    /**\n     * The record a frame merges into: the existing one of its id, or a new one.\n     * @param kind - the frame type\n     * @param id - the id\n     * @param line - the frame's line\n     * @returns the record\n     */\n    private recordFor(kind: FrameKind, id: string, line: number): NodeRecord {\n        const map = kind === \"Typedef\" ? this.typedefs : this.nodes;\n        const existing = map.get(id);\n        if (existing !== undefined) {\n            if (existing.kind !== kind) {\n                this.tally(\n                    \"validation-error\",\n                    OBO_ISSUE.ID_KIND_CLASH,\n                    `an id names both a ${existing.kind} and an ${kind}; the ${existing.kind} is the node`,\n                    id,\n                    line,\n                );\n            } else {\n                this.tally(\n                    \"merged\",\n                    OBO_ISSUE.DUPLICATE_NODE,\n                    `[${kind}] frames with this id are merged (spec 4.1.1)`,\n                    id,\n                    line,\n                );\n            }\n            return existing;\n        }\n        const created: NodeRecord = {\n            id,\n            kind,\n            line,\n            values: new Map(),\n            lists: new Map(),\n            edges: [],\n            seen: new Set(),\n            raw: ownRecord<string[]>(),\n        };\n        map.set(id, created);\n        return created;\n    }\n\n    /**\n     * A clause's tag (a 1.0 tag read as its current one), the synonym scope that tag implies, its\n     * qualifier block and its value, with the syntax warnings about stray braces recorded.\n     * @param clause - the clause\n     * @returns the parts\n     */\n    private clauseParts(clause: Clause): {\n        tag: string;\n        scope: string | null;\n        qualifiers: ReturnType<typeof splitQualifiers>[\"qualifiers\"];\n        value: string;\n    } {\n        let { tag } = clause;\n        let scope: string | null = null;\n        const deprecated = DEPRECATED_TAGS.get(tag);\n        if (deprecated !== undefined) {\n            this.tally(\n                \"coercion\",\n                OBO_ISSUE.DEPRECATED_TAG,\n                `the 1.0 tag is read as ${deprecated[0]}`,\n                tag,\n                clause.line,\n            );\n            [tag, scope] = deprecated;\n        }\n        let split = splitQualifiers(clause.value);\n        const open = ID_VALUE_TAGS.has(tag) ? unclosedBlock(split.value) : -1;\n        if (open >= 0) {\n            this.tally(\n                \"parse-error\",\n                OBO_ISSUE.SYNTAX,\n                \"a qualifier block without its closing brace was dropped\",\n                tag,\n                clause.line,\n            );\n            split = splitQualifiers(split.value.slice(0, open).trimEnd());\n        }\n        const { qualifiers } = split;\n        if (split.badBlock !== null) {\n            this.tally(\n                \"parse-error\",\n                OBO_ISSUE.SYNTAX,\n                \"a closing brace that is not a qualifier block was kept as text\",\n                tag,\n                clause.line,\n            );\n        } else if (hasStrayBrace(split.value)) {\n            this.tally(\n                \"parse-error\",\n                OBO_ISSUE.SYNTAX,\n                \"an unescaped brace inside a value was kept as text\",\n                tag,\n                clause.line,\n            );\n        }\n        return { tag, scope, qualifiers, value: split.value };\n    }\n\n    /**\n     * A def, expand_assertion_to or expand_expression_to clause: quoted text and its xref list.\n     * @param record - the record\n     * @param tag - the tag\n     * @param value - the clause value\n     * @param tokens - its tokens\n     * @param qualifiers - its qualifier block\n     * @param line - its line\n     */\n    private definition(\n        record: NodeRecord,\n        tag: string,\n        value: string,\n        tokens: ReturnType<typeof tokenize>,\n        qualifiers: ReturnType<typeof splitQualifiers>[\"qualifiers\"],\n        line: number,\n    ): void {\n        if (tag === \"def\" && record.values.has(\"def\")) {\n            // the second def of an id: reported, and none of its xrefs leak into the first's\n            this.single(record, \"def\", null, line);\n            return;\n        }\n        const text = this.quotedWithXrefs(record, tag, value, tokens, line);\n        if (tag === \"def\") {\n            this.single(record, \"def\", text.text, line, () => {\n                record.values.set(\"def.xrefs\", text.xrefs);\n            });\n            this.extraQualifiers(record, tag, text.text, qualifiers);\n        } else {\n            this.push(record, tag, withQualifiers({ template: text.text, xrefs: text.xrefs }, qualifiers));\n        }\n    }\n\n    /**\n     * Apply one clause to a record.\n     * @param record - the record\n     * @param clause - the clause\n     */\n    private applyClause(record: NodeRecord, clause: Clause): void {\n        const key = `${clause.tag}\\u0000${clause.value}`;\n        if (record.seen.has(key)) {\n            return;\n        }\n        record.seen.add(key);\n        if (record.kind === \"Typedef\") {\n            append(record.raw, clause.tag, clause.value);\n        }\n        const { tag, scope, qualifiers, value } = this.clauseParts(clause);\n        // a control character kept in the value is the shared W_CONTROL_CHARACTER of the text check\n        const where = { line: clause.line, element: record.id };\n        if (TYPEDEF_TAGS.has(tag) && record.kind !== \"Typedef\") {\n            this.unrecognized(record, clause);\n            return;\n        }\n        if (TEXT_TAGS.has(tag)) {\n            this.text(record, tag, value, qualifiers, clause.line);\n            return;\n        }\n        if (BOOL_TAGS.has(tag)) {\n            const text = unescapeObo(value).trim();\n            if (text !== \"true\" && text !== \"false\") {\n                this.report.error(\n                    \"validation-error\",\n                    OBO_ISSUE.BAD_VALUE,\n                    `${tag}: ${JSON.stringify(text)} is not true or false; the clause is skipped`,\n                    where,\n                );\n                return;\n            }\n            this.single(record, tag, text === \"true\", clause.line);\n            this.extraQualifiers(record, tag, text, qualifiers);\n            return;\n        }\n        const tokens = tokenize(value);\n        if (ID_LIST_TAGS.has(tag)) {\n            const id = this.oneWord(tokens, tag, where);\n            if (id !== null) {\n                this.push(record, tag, id);\n                this.extraQualifiers(record, tag, id, qualifiers);\n                if (tag === \"subset\" && !this.subsets.has(id)) {\n                    this.tally(\n                        \"validation-error\",\n                        OBO_ISSUE.UNDECLARED,\n                        \"a subset no subsetdef declares\",\n                        id,\n                        clause.line,\n                    );\n                }\n            }\n            return;\n        }\n        switch (tag) {\n            case \"is_a\":\n            case \"instance_of\": {\n                if (tag === \"instance_of\" && record.kind !== \"Instance\") {\n                    this.unrecognized(record, clause);\n                    return;\n                }\n                const target = this.oneWord(tokens, tag, where);\n                if (target !== null) {\n                    record.edges.push({ relation: tag, target, qualifiers, line: clause.line });\n                }\n                return;\n            }\n            case \"relationship\": {\n                if (tokens.length !== 2 || tokens.some((t) => t.kind !== \"word\")) {\n                    this.report.error(\n                        \"validation-error\",\n                        OBO_ISSUE.BAD_VALUE,\n                        `relationship needs a relation and a target, found ${JSON.stringify(unescapeObo(value))}; the clause is skipped`,\n                        where,\n                    );\n                    return;\n                }\n                record.edges.push({ relation: tokens[0].text, target: tokens[1].text, qualifiers, line: clause.line });\n                return;\n            }\n            case \"intersection_of\": {\n                if (tokens.length < 1 || tokens.length > 2 || tokens.some((t) => t.kind !== \"word\")) {\n                    this.report.error(\n                        \"validation-error\",\n                        OBO_ISSUE.BAD_VALUE,\n                        `intersection_of needs a class, or a relation and a class, found ${JSON.stringify(unescapeObo(value))}; the clause is skipped`,\n                        where,\n                    );\n                    return;\n                }\n                const item: Record<string, unknown> =\n                    tokens.length === 1\n                        ? { relation: null, target: tokens[0].text }\n                        : { relation: tokens[0].text, target: tokens[1].text };\n                this.push(record, tag, withQualifiers(item, qualifiers));\n                return;\n            }\n            case \"holds_over_chain\":\n            case \"equivalent_to_chain\": {\n                if (tokens.length !== 2 || tokens.some((t) => t.kind !== \"word\")) {\n                    this.report.error(\n                        \"validation-error\",\n                        OBO_ISSUE.BAD_VALUE,\n                        `${tag} needs two relations; the clause is skipped`,\n                        where,\n                    );\n                    return;\n                }\n                this.push(record, tag, [tokens[0].text, tokens[1].text]);\n                this.extraQualifiers(record, tag, `${tokens[0].text} ${tokens[1].text}`, qualifiers);\n                return;\n            }\n            case \"def\":\n            case \"expand_assertion_to\":\n            case \"expand_expression_to\":\n                this.definition(record, tag, value, tokens, qualifiers, clause.line);\n                return;\n            case \"synonym\":\n                this.synonym(record, tokens, scope, qualifiers, clause.line);\n                return;\n            case \"xref\": {\n                const xref = parseXref(value);\n                if (xref === null) {\n                    this.report.error(\n                        \"validation-error\",\n                        OBO_ISSUE.BAD_VALUE,\n                        \"xref has no id; the clause is skipped\",\n                        where,\n                    );\n                    return;\n                }\n                this.push(record, \"xref\", xref.id);\n                this.describe(record, [xref], tag, clause.line);\n                this.extraQualifiers(record, tag, xref.id, qualifiers ?? xref.qualifiers);\n                return;\n            }\n            case \"property_value\":\n                this.propertyValue(record, tokens, qualifiers, where);\n                return;\n            default:\n                this.unrecognized(record, clause);\n        }\n    }\n\n    /**\n     * A single-valued text clause (name, comment, ...), warning about a quote that never closes\n     * (stripComment() then keeps a `!` comment after it as text).\n     * @param record - the record\n     * @param tag - the tag\n     * @param value - the raw value\n     * @param qualifiers - its qualifier block\n     * @param line - its line\n     */\n    private text(record: NodeRecord, tag: string, value: string, qualifiers: Qualifiers | null, line: number): void {\n        if (tokenize(value).some((t) => t.kind === \"quoted\" && t.unterminated)) {\n            this.tally(\n                \"parse-error\",\n                OBO_ISSUE.SYNTAX,\n                \"an unterminated quote; the text after it, a comment included, is kept\",\n                tag,\n                line,\n            );\n        }\n        const text = unescapeObo(value).trim();\n        this.single(record, tag, text, line);\n        this.extraQualifiers(record, tag, text, qualifiers);\n    }\n\n    /**\n     * Read a value that must be one word.\n     * @param tokens - the value's tokens\n     * @param tag - the tag, for the message\n     * @param where - the location\n     * @returns the word, or null after reporting E_BAD_VALUE\n     */\n    private oneWord(tokens: readonly Token[], tag: string, where: Where): string | null {\n        if (tokens.length === 1 && tokens[0].kind === \"word\") {\n            return tokens[0].text;\n        }\n        const found = tokens.map((t) => t.text).join(\" \");\n        this.report.error(\n            \"validation-error\",\n            OBO_ISSUE.BAD_VALUE,\n            `${tag} needs one id, found ${JSON.stringify(found)}; the clause is skipped`,\n            where,\n        );\n        return null;\n    }\n\n    /**\n     * Read `\"text\" [xrefs]` (def, expand_*), reporting the forms the grammar does not allow.\n     * @param record - the record (xref descriptions go to its `xref.descriptions`)\n     * @param tag - the tag\n     * @param value - the raw value\n     * @param tokens - its tokens\n     * @param line - the line\n     * @returns the text and the xref ids\n     */\n    private quotedWithXrefs(\n        record: NodeRecord,\n        tag: string,\n        value: string,\n        tokens: readonly Token[],\n        line: number,\n    ): { text: string; xrefs: string[] } {\n        if (tokens.length === 0 || tokens[0].kind !== \"quoted\") {\n            this.tally(\"parse-error\", OBO_ISSUE.SYNTAX, \"the text is not quoted; the whole value is kept\", tag, line);\n            return { text: unescapeObo(value).trim(), xrefs: [] };\n        }\n        if (tokens[0].unterminated) {\n            this.tally(\n                \"parse-error\",\n                OBO_ISSUE.SYNTAX,\n                \"an unterminated quote; the text runs to the end of the line\",\n                tag,\n                line,\n            );\n            return { text: tokens[0].text, xrefs: [] };\n        }\n        const list = tokens[1];\n        if (list?.kind !== \"list\") {\n            this.tally(\"parse-error\", OBO_ISSUE.SYNTAX, \"the xref list is missing\", tag, line);\n            return { text: tokens[0].text, xrefs: [] };\n        }\n        if (list.unterminated) {\n            this.tally(\"parse-error\", OBO_ISSUE.SYNTAX, \"an xref list without its closing ]; kept as read\", tag, line);\n        }\n        if (tokens.length > 2) {\n            this.tally(\"parse-error\", OBO_ISSUE.SYNTAX, \"text after the xref list was ignored\", tag, line);\n        }\n        const xrefs = parseXrefList(list.text);\n        this.describe(record, xrefs, tag, line);\n        this.xrefQualifiers(record, tag, xrefs);\n        return { text: tokens[0].text, xrefs: xrefs.map((x) => x.id) };\n    }\n\n    /**\n     * Read a synonym: `\"text\" SCOPE? TYPE? [xrefs]` (the scope optional in 1.2).\n     * @param record - the record\n     * @param tokens - the value's tokens\n     * @param fixedScope - the scope of a 1.0 tag (exact_synonym), or null\n     * @param qualifiers - the clause's qualifiers\n     * @param line - the line\n     */\n    private synonym(\n        record: NodeRecord,\n        tokens: readonly Token[],\n        fixedScope: string | null,\n        qualifiers: Qualifiers | null,\n        line: number,\n    ): void {\n        if (tokens.length === 0 || tokens[0].kind !== \"quoted\") {\n            this.report.error(\n                \"validation-error\",\n                OBO_ISSUE.BAD_VALUE,\n                \"a synonym needs its quoted text; the clause is skipped\",\n                {\n                    line,\n                    element: record.id,\n                },\n            );\n            return;\n        }\n        if (tokens[0].unterminated) {\n            this.tally(\n                \"parse-error\",\n                OBO_ISSUE.SYNTAX,\n                \"an unterminated quote; the text runs to the end of the line\",\n                \"synonym\",\n                line,\n            );\n        }\n        const words = tokens\n            .slice(1)\n            .filter((t) => t.kind === \"word\")\n            .map((t) => t.text);\n        const list = tokens.slice(1).find((t) => t.kind === \"list\");\n        let scope: string | null = fixedScope;\n        let type: string | null = null;\n        if (fixedScope === null) {\n            if (words.length > 0 && SYNONYM_SCOPES.has(words[0])) {\n                [scope] = words;\n                type = words[1] ?? null;\n            } else if (words.length > 0 && this.synonymTypes.has(words[0])) {\n                [type] = words;\n                scope = \"RELATED\";\n            } else if (words.length > 0) {\n                [type] = words;\n                this.tally(\n                    \"validation-error\",\n                    OBO_ISSUE.SYNONYM_SCOPE,\n                    `a scope that is not EXACT, BROAD, NARROW or RELATED was kept as the type, scope null`,\n                    words[0],\n                    line,\n                );\n            } else {\n                scope = \"RELATED\";\n            }\n            if (scope === \"RELATED\" && (words.length === 0 || words[0] === type) && !this.allowsMissingScope()) {\n                this.tally(\n                    \"validation-error\",\n                    OBO_ISSUE.SYNONYM_SCOPE,\n                    \"a synonym without a scope (1.2 only) is read as RELATED\",\n                    \"synonym\",\n                    line,\n                );\n            }\n        }\n        if (type !== null) {\n            const declared = this.synonymTypes.get(type);\n            if (declared === undefined) {\n                if (scope !== null) {\n                    this.tally(\n                        \"validation-error\",\n                        OBO_ISSUE.UNDECLARED,\n                        \"a synonym type no synonymtypedef declares\",\n                        type,\n                        line,\n                    );\n                }\n            } else if (declared !== null) {\n                // the 1.2 guide: a type's default scope is used regardless of the synonym's own\n                scope = declared;\n            }\n        }\n        if (words.length > 2 || list === undefined) {\n            this.tally(\n                \"parse-error\",\n                OBO_ISSUE.SYNTAX,\n                list === undefined ? \"a synonym without its xref list\" : \"extra words after the synonym type\",\n                \"synonym\",\n                line,\n            );\n        }\n        const listAt = list === undefined ? -1 : tokens.indexOf(list);\n        const stray = tokens.some(\n            (t, k) =>\n                k > 0 && (t.kind === \"quoted\" || (t.kind === \"list\" && k !== listAt) || (listAt >= 0 && k > listAt)),\n        );\n        if (stray) {\n            this.tally(\n                \"parse-error\",\n                OBO_ISSUE.SYNTAX,\n                \"a second quoted string, a second xref list or text after the list was ignored\",\n                \"synonym\",\n                line,\n            );\n        }\n        if (list?.unterminated === true) {\n            this.tally(\n                \"parse-error\",\n                OBO_ISSUE.SYNTAX,\n                \"an xref list without its closing ]; kept as read\",\n                \"synonym\",\n                line,\n            );\n        }\n        const xrefs = list === undefined ? [] : parseXrefList(list.text);\n        this.describe(record, xrefs, \"synonym\", line);\n        this.xrefQualifiers(record, \"synonym\", xrefs);\n        this.push(\n            record,\n            \"synonym\",\n            withQualifiers({ text: tokens[0].text, scope, type, xrefs: xrefs.map((x) => x.id) }, qualifiers),\n        );\n    }\n\n    /**\n     * Whether the file's version lets a synonym omit its scope (1.0 and 1.2).\n     * @returns true for a 1.2 or 1.0 file\n     */\n    private allowsMissingScope(): boolean {\n        return this.version !== null && /^(1\\.[0-2]|GO_1\\.[0-2])\\b/.test(this.version);\n    }\n\n    /**\n     * Read a property_value: `relation \"literal\" datatype` or `relation id`.\n     * @param record - the record\n     * @param tokens - the value's tokens\n     * @param qualifiers - the clause's qualifiers\n     * @param where - the location\n     */\n    private propertyValue(\n        record: NodeRecord,\n        tokens: readonly Token[],\n        qualifiers: Qualifiers | null,\n        where: Where,\n    ): void {\n        if (tokens.length < 2 || tokens.length > 3 || tokens[0].kind !== \"word\" || tokens[1].kind === \"list\") {\n            this.report.error(\n                \"validation-error\",\n                OBO_ISSUE.BAD_VALUE,\n                \"property_value needs a relation and a value; the clause is skipped\",\n                where,\n            );\n            return;\n        }\n        if (tokens.some((t) => t.unterminated)) {\n            this.tally(\n                \"parse-error\",\n                OBO_ISSUE.SYNTAX,\n                \"an unterminated quote; the text runs to the end of the line\",\n                \"property_value\",\n                where.line,\n            );\n        }\n        let datatype = tokens.length === 3 ? tokens[2].text : null;\n        if (tokens.length === 3 && tokens[2].kind !== \"word\") {\n            this.tally(\n                \"parse-error\",\n                OBO_ISSUE.SYNTAX,\n                \"a datatype that is not a word was ignored\",\n                \"property_value\",\n                where.line,\n            );\n            datatype = null;\n        }\n        this.push(\n            record,\n            \"property_value\",\n            withQualifiers({ relation: tokens[0].text, value: tokens[1].text, datatype }, qualifiers),\n        );\n    }\n\n    /**\n     * Set a single-valued column, keeping the first value of an id.\n     * @param record - the record\n     * @param column - the column\n     * @param value - the value\n     * @param line - the line\n     * @param also - more to set together with the value\n     */\n    private single(record: NodeRecord, column: string, value: unknown, line: number, also?: () => void): void {\n        if (record.values.has(column)) {\n            this.tally(\n                \"validation-error\",\n                OBO_ISSUE.DUPLICATE_ATTRIBUTE,\n                \"a single-valued tag given twice for one id; the first is kept\",\n                column,\n                line,\n            );\n            return;\n        }\n        record.values.set(column, value);\n        also?.();\n    }\n\n    /**\n     * Append to a list column, without repeats (merged frames take the union).\n     * @param record - the record\n     * @param column - the column\n     * @param value - the item\n     */\n    private push(record: NodeRecord, column: string, value: unknown): void {\n        let list = record.lists.get(column);\n        if (list === undefined) {\n            list = [];\n            record.lists.set(column, list);\n        }\n        // objects are never repeated: identical clauses were already skipped\n        if (typeof value === \"object\" || !list.includes(value)) {\n            list.push(value);\n        }\n    }\n\n    /**\n     * Record xref descriptions in `xref.descriptions` (the first description of an id is kept),\n     * warning about a description whose quote never closes.\n     * @param target - the record\n     * @param xrefs - the xrefs\n     * @param tag - the clause's tag\n     * @param line - the clause's line\n     */\n    private describe(target: NodeRecord, xrefs: readonly Xref[], tag: string, line: number): void {\n        for (const xref of xrefs) {\n            if (xref.unterminated) {\n                this.tally(\n                    \"parse-error\",\n                    OBO_ISSUE.SYNTAX,\n                    \"an xref description whose quote never closes runs to the end\",\n                    tag,\n                    line,\n                );\n            }\n            if (xref.description !== null) {\n                let map = target.values.get(\"xref.descriptions\") as Record<string, string> | undefined;\n                if (map === undefined) {\n                    map = ownRecord<string>();\n                    target.values.set(\"xref.descriptions\", map);\n                }\n                if (!Object.hasOwn(map, xref.id)) {\n                    map[xref.id] = xref.description;\n                }\n            }\n        }\n    }\n\n    /**\n     * Keep the per-xref qualifiers of an xref list (OBO 1.2: `[A:1 {source=\"x\"}]`) in\n     * `obo.qualifiers` under `<tag>.xrefs`.\n     * @param record - the record\n     * @param tag - the clause's tag\n     * @param xrefs - the list's xrefs\n     */\n    private xrefQualifiers(record: NodeRecord, tag: string, xrefs: readonly Xref[]): void {\n        for (const xref of xrefs) {\n            this.extraQualifiers(record, `${tag}.xrefs`, xref.id, xref.qualifiers);\n        }\n    }\n\n    /**\n     * Keep the qualifiers of a clause whose column has no place for them in `obo.qualifiers`.\n     * @param record - the record\n     * @param tag - the tag\n     * @param value - the clause's value as stored\n     * @param qualifiers - the qualifiers, or null\n     */\n    private extraQualifiers(record: NodeRecord, tag: string, value: string, qualifiers: Qualifiers | null): void {\n        if (qualifiers === null) {\n            return;\n        }\n        const map = (record.values.get(\"obo.qualifiers\") as Record<string, unknown[]> | undefined) ?? {};\n        (map[tag] ??= []).push({ value, qualifiers });\n        record.values.set(\"obo.qualifiers\", map);\n    }\n\n    /**\n     * Keep an unknown clause in `obo.unrecognized`.\n     * @param record - the record\n     * @param clause - the clause\n     */\n    private unrecognized(record: NodeRecord, clause: Clause): void {\n        let map = record.values.get(\"obo.unrecognized\") as Record<string, string[]> | undefined;\n        if (map === undefined) {\n            map = ownRecord<string[]>();\n            record.values.set(\"obo.unrecognized\", map);\n        }\n        append(map, clause.tag, unescapeObo(clause.value));\n        this.tally(\n            \"validation-error\",\n            OBO_ISSUE.UNKNOWN_ELEMENT,\n            \"an unknown tag was kept in obo.unrecognized\",\n            clause.tag,\n            clause.line,\n        );\n    }\n\n    /**\n     * Count a warning, recorded once per code and element at the end.\n     * @param category - the category\n     * @param code - the code\n     * @param what - what happened\n     * @param element - the tag, id or name it is about\n     * @param line - the first line\n     */\n    tally(category: Tally[\"category\"], code: string, what: string, element: string, line: number): void {\n        const key = `${code}\\u0000${element}\\u0000${what}`;\n        const found = this.tallies.get(key);\n        if (found === undefined) {\n            this.tallies.set(key, { category, code, element, what, line, count: 1 });\n        } else {\n            found.count++;\n        }\n    }\n\n    /**\n     * Record the counted warnings, in the order they were first seen; past MAX_TALLIES_PER_CODE\n     * of one code, the rest are summed up in one warning.\n     */\n    flushTallies(): void {\n        const listed = new Map<string, number>();\n        const over = new Map<string, Tally[]>();\n        for (const t of this.tallies.values()) {\n            const n = (listed.get(t.code) ?? 0) + 1;\n            listed.set(t.code, n);\n            if (n > MAX_TALLIES_PER_CODE) {\n                const rest = over.get(t.code) ?? [];\n                rest.push(t);\n                over.set(t.code, rest);\n                continue;\n            }\n            this.report.warning(\n                t.category,\n                t.code,\n                `${t.element}: ${t.what} (${t.count} time${plural(t.count)}, first at line ${t.line})`,\n                {\n                    line: t.line,\n                    element: t.element,\n                },\n            );\n        }\n        for (const [code, rest] of over) {\n            this.report.warning(\n                rest[0].category,\n                code,\n                `${rest.length} more element${plural(rest.length)} with this warning, not listed (first: ${rest[0].element}: ${rest[0].what}, line ${rest[0].line})`,\n                { line: rest[0].line },\n            );\n        }\n        this.tallies.clear();\n    }\n\n    /**\n     * The first line that makes the input not OBO: null unless no frame header and no plausible\n     * header tag was read while some line was neither (an HTML page, a JSON, GML, DOT or CSV file,\n     * UTF-16 read without its BOM). A file of only comments is OBO, if an empty one.\n     * @returns the line, or null\n     */\n    notObo(): number | null {\n        return this.frameSeen || this.tagClauses > 0 ? null : this.firstBadLine;\n    }\n\n    /**\n     * Warn about the header once the file is read: a missing or unknown format-version (the\n     * synonym-scope rule depends on it), a date that is not a real calendar date.\n     */\n    checkHeader(): void {\n        if (this.version === null) {\n            const empty = this.frameSeen ? \"\" : \" and the file has no frames: nothing was read\";\n            this.tally(\n                \"validation-error\",\n                OBO_ISSUE.FORMAT_VERSION,\n                `the header has no format-version (required by 1.2 and 1.4)${empty}; read as the 1.0 / 1.2 / 1.4 union`,\n                \"format-version\",\n                1,\n            );\n        } else if (!KNOWN_VERSION.test(this.version)) {\n            this.tally(\n                \"validation-error\",\n                OBO_ISSUE.FORMAT_VERSION,\n                `format-version ${JSON.stringify(this.version)} is not 1.0, 1.2 or 1.4; read as 1.4`,\n                \"format-version\",\n                1,\n            );\n        }\n        const date = this.header.date?.[0];\n        if (\n            date !== undefined &&\n            /^\\d{2}:\\d{2}:\\d{4}\\s+\\d{2}:\\d{2}$/.test(date.trim()) &&\n            oboDate(date.trim()) === null\n        ) {\n            this.tally(\n                \"validation-error\",\n                OBO_ISSUE.SYNTAX,\n                \"the header date is not a real calendar date; created is null\",\n                \"date\",\n                1,\n            );\n        }\n    }\n\n    /**\n     * The header as GraphMeta fields (design 4.2): name from `ontology`, the version, `created` from\n     * the `dd:MM:yyyy HH:mm` date, `creator` from `saved-by`.\n     * @returns the metadata patch, without `extra`\n     */\n    meta(): GraphMetaPatch {\n        const first = (tag: string): string | null => {\n            const values = this.header[tag];\n            return values === undefined ? null : unescapeObo(values[0]).trim();\n        };\n        return {\n            name: first(\"ontology\"),\n            sourceFormat: \"obo\",\n            sourceVersion: this.version,\n            created: oboDate(first(\"date\")),\n            creator: first(\"saved-by\"),\n        };\n    }\n\n    /**\n     * The raw header clauses.\n     * @returns the header by tag\n     */\n    headerRecord(): Record<string, string[]> {\n        return this.header;\n    }\n\n    /**\n     * The namespace a frame without one gets.\n     * @returns the default namespace, or null\n     */\n    namespaceDefault(): string | null {\n        return this.defaultNamespace;\n    }\n}\n\n/**\n * Add the qualifiers to a json item when there are any.\n * @param item - the item\n * @param qualifiers - the qualifiers, or null\n * @returns the item\n */\nfunction withQualifiers(item: Record<string, unknown>, qualifiers: Qualifiers | null): Record<string, unknown> {\n    return qualifiers === null ? item : { ...item, qualifiers };\n}\n\n/**\n * The OBO header date `dd:MM:yyyy HH:mm` as ISO 8601 (`yyyy-MM-ddTHH:mm`).\n * @param text - the header value, or null\n * @returns the ISO text, or null when the date is not of that form\n */\nfunction oboDate(text: string | null): string | null {\n    const m = text === null ? null : /^(\\d{2}):(\\d{2}):(\\d{4})\\s+(\\d{2}):(\\d{2})$/.exec(text);\n    if (m === null) {\n        return null;\n    }\n    const [, dd, mm, yyyy, hh, min] = m;\n    // a real calendar date: 31:02 and 31:04 do not survive the round trip through Date\n    const day = new Date(Date.UTC(Number(yyyy), Number(mm) - 1, Number(dd)));\n    if (Number(mm) < 1 || Number(mm) > 12 || day.getUTCDate() !== Number(dd) || Number(hh) > 23 || Number(min) > 59) {\n        return null;\n    }\n    return `${yyyy}-${mm}-${dd}T${hh}:${min}`;\n}\n\n/** What writeGraph() pushes, decided before anything reaches the sink. */\ninterface GraphPlan {\n    /** The node records, in first-appearance order. */\n    readonly nodes: readonly NodeRecord[];\n    /** The undeclared targets that become placeholder nodes. */\n    readonly placeholders: readonly string[];\n    /** The edges to push. */\n    readonly edges: readonly { readonly source: string; readonly edge: PendingEdge }[];\n}\n\n/**\n * Decide what is written (design 4.2): the node records (Typedefs too under typedefs \"nodes\", the\n * obsolete ones left out under obsolete \"drop\"), the placeholders of undeclared targets and the\n * edges; record the warnings that need the whole file (obsoletion rules, undeclared relations,\n * dangling targets, dropped obsolete terms).\n * @param reader - the finished reader\n * @param report - the report\n * @param addMissingNodes - whether an undeclared target becomes a placeholder node\n * @param obo - the OBO options\n * @returns the plan\n */\nfunction planGraph(\n    reader: OboReader,\n    report: ImportReportBuilder,\n    addMissingNodes: boolean,\n    obo: ResolvedOboOptions,\n): GraphPlan {\n    const records: NodeRecord[] = [...reader.nodes.values()];\n    for (const [id, typedef] of reader.typedefs) {\n        const node = reader.nodes.get(id);\n        if (node !== undefined) {\n            reader.tally(\n                \"validation-error\",\n                OBO_ISSUE.ID_KIND_CLASH,\n                `an id names both a ${node.kind} and a Typedef; the ${node.kind} is the node`,\n                id,\n                typedef.line,\n            );\n        } else if (obo.typedefs === \"nodes\") {\n            records.push(typedef);\n        }\n    }\n    // a class expression needs two or more operands, counted after merging (spec 4.1.1)\n    for (const record of [...reader.nodes.values(), ...reader.typedefs.values()]) {\n        for (const tag of [\"intersection_of\", \"union_of\"]) {\n            if (record.lists.get(tag)?.length === 1) {\n                reader.tally(\n                    \"validation-error\",\n                    OBO_ISSUE.CARDINALITY,\n                    \"a single clause (a class expression needs two or more)\",\n                    tag,\n                    record.line,\n                );\n            }\n        }\n    }\n    const dropped = new Set<string>();\n    const kept = new Set<string>();\n    for (const record of records) {\n        const obsolete = record.values.get(\"is_obsolete\") === true;\n        (obo.obsolete === \"drop\" && obsolete ? dropped : kept).add(record.id);\n        // obsoletion rules (the 1.2 guide; fastobo-validator --obsoletion)\n        if (obsolete && record.edges.length > 0) {\n            reader.tally(\n                \"validation-error\",\n                OBO_ISSUE.OBSOLETION,\n                \"an obsolete term has is_a or relationship clauses; they are kept\",\n                \"is_obsolete\",\n                record.edges[0].line,\n            );\n        }\n        if (!obsolete && (record.lists.has(\"replaced_by\") || record.lists.has(\"consider\"))) {\n            reader.tally(\n                \"validation-error\",\n                OBO_ISSUE.OBSOLETION,\n                \"replaced_by or consider on a term that is not obsolete; kept\",\n                \"replaced_by\",\n                record.line,\n            );\n        }\n    }\n    const declared = new Set<string>(reader.typedefs.keys());\n    for (const typedef of reader.typedefs.values()) {\n        for (const xref of (typedef.lists.get(\"xref\") ?? []) as string[]) {\n            declared.add(xref);\n        }\n    }\n    const dangling: string[] = [];\n    const danglingSet = new Set<string>();\n    let danglingEdges = 0;\n    let droppedEdges = 0;\n    const edges: { source: string; edge: PendingEdge }[] = [];\n    for (const record of records) {\n        for (const edge of record.edges) {\n            if (dropped.has(record.id) || dropped.has(edge.target)) {\n                droppedEdges++;\n                continue;\n            }\n            if (!BUILTIN_RELATIONS.has(edge.relation) && !declared.has(edge.relation)) {\n                reader.tally(\n                    \"validation-error\",\n                    OBO_ISSUE.UNDECLARED,\n                    \"a relation no Typedef declares\",\n                    edge.relation,\n                    edge.line,\n                );\n            }\n            if (!kept.has(edge.target)) {\n                if (!danglingSet.has(edge.target)) {\n                    danglingSet.add(edge.target);\n                    dangling.push(edge.target);\n                }\n                if (!addMissingNodes) {\n                    danglingEdges++;\n                    report.counts.skippedEdges++;\n                    continue;\n                }\n            }\n            edges.push({ source: record.id, edge });\n        }\n    }\n    reader.flushTallies();\n    reportDangling(records, dangling, addMissingNodes, danglingEdges, report, new Set(reader.typedefs.keys()));\n    if (dropped.size > 0) {\n        report.warning(\n            \"merged\",\n            OBO_ISSUE.OBSOLETE_DROPPED,\n            `${dropped.size} obsolete term${plural(dropped.size)} and ${droppedEdges} edge${plural(droppedEdges)} to or from them were left out (obsolete: \"drop\")`,\n            { element: [...dropped][0] },\n        );\n    }\n    return {\n        nodes: records.filter((record) => kept.has(record.id)),\n        placeholders: addMissingNodes ? dangling : [],\n        edges,\n    };\n}\n\n/**\n * Record the one W_DANGLING_REFERENCE of an import: the count, the first targets, and for a target\n * that is another term's alt_id, the term it is an alt_id of.\n * @param records - every node record\n * @param dangling - the undeclared targets, in first-reference order\n * @param addMissingNodes - whether they became placeholder nodes\n * @param droppedEdges - the edges dropped under addMissingNodes false\n * @param report - the report\n * @param typedefs - the ids of the Typedef frames (kept as metadata, so not nodes)\n */\nfunction reportDangling(\n    records: readonly NodeRecord[],\n    dangling: readonly string[],\n    addMissingNodes: boolean,\n    droppedEdges: number,\n    report: ImportReportBuilder,\n    typedefs: ReadonlySet<string>,\n): void {\n    if (dangling.length === 0) {\n        return;\n    }\n    const altOf = new Map<string, string>();\n    for (const record of records) {\n        for (const alt of (record.lists.get(\"alt_id\") ?? []) as string[]) {\n            altOf.set(alt, record.id);\n        }\n    }\n    const shown = dangling.slice(0, 5).map((id) => {\n        const primary = altOf.get(id);\n        if (typedefs.has(id)) {\n            return `${id} (a Typedef, kept as metadata, not a node)`;\n        }\n        return primary === undefined ? id : `${id} (an alt_id of ${primary})`;\n    });\n    const more = dangling.length > 5 ? `, ... (${dangling.length - 5} more)` : \"\";\n    const action = addMissingNodes\n        ? \"each became a placeholder node (graphty.placeholder)\"\n        : `${droppedEdges} edge${plural(droppedEdges)} to them ${agree(droppedEdges, \"was\", \"were\")} dropped (addMissingNodes false)`;\n    report.warning(\n        \"validation-error\",\n        OBO_ISSUE.DANGLING_REFERENCE,\n        `${dangling.length} target${plural(dangling.length)} no frame declares: ${shown.join(\", \")}${more}; ${action}`,\n        { element: dangling[0] },\n    );\n}\n\n/** Pushes ids into a sink: the id coercion rule and the cancellation check. */\nclass Pusher {\n    readonly sink: GraphSink;\n\n    readonly report: ImportReportBuilder;\n\n    private readonly coercer: IdCoercer;\n\n    private readonly signal: AbortSignal | null;\n\n    /** The original ids restored under restoreMangledIds, by the id the file wrote. */\n    readonly restored = new Map<string, string>();\n\n    private since = 0;\n\n    /**\n     * Create a pusher.\n     * @param sink - the sink\n     * @param report - the report\n     * @param options - the resolved common options\n     */\n    constructor(sink: GraphSink, report: ImportReportBuilder, options: ReturnType<typeof resolveImportOptions>) {\n        this.sink = sink;\n        this.report = report;\n        this.coercer = new IdCoercer(options.ids);\n        this.signal = options.signal;\n    }\n\n    /**\n     * An id text under the `ids` rule, reporting a merge.\n     * @param text - the id as written\n     * @returns the node id\n     */\n    id(text: string): NodeId {\n        const id = this.coercer.text(this.restored.get(text) ?? text);\n        const merge = this.coercer.lastMerge;\n        if (merge !== null) {\n            this.report.warning(\n                \"coercion\",\n                OBO_ISSUE.ID_MERGED,\n                `id text ${JSON.stringify(merge.text)} merged with ${JSON.stringify(merge.previousText)} as ${merge.id}`,\n                { element: text },\n            );\n        }\n        return id;\n    }\n\n    /**\n     * Add a node, counting it, or record why it was refused.\n     * @param text - the id as written\n     * @param line - the line, when known\n     * @returns the node index, or -1 when refused\n     */\n    node(text: string, line?: number): number {\n        this.tick();\n        try {\n            const id = this.id(text);\n            const known = this.sink.indexOf(id) !== INVALID_INDEX;\n            const index = this.sink.addNode(id);\n            if (!known) {\n                this.report.counts.nodes++;\n            }\n            return index;\n        } catch (err) {\n            this.report.recordError(err, { line, element: text });\n            this.report.counts.skippedNodes++;\n            return -1;\n        }\n    }\n\n    /** Check the cancellation signal every ABORT_CHECK_INTERVAL pushes. */\n    tick(): void {\n        if (++this.since >= ABORT_CHECK_INTERVAL) {\n            this.since = 0;\n            throwIfAborted(this.signal);\n        }\n    }\n}\n\n/**\n * Write the records into the sink (design 4.2): the nodes with the vocabulary columns they use,\n * the placeholders of undeclared targets, then the edges.\n * @param reader - the finished reader\n * @param sink - the sink\n * @param report - the report\n * @param options - the resolved options\n * @param obo - the OBO options\n */\nfunction writeGraph(\n    reader: OboReader,\n    sink: GraphSink,\n    report: ImportReportBuilder,\n    options: ReturnType<typeof resolveImportOptions>,\n    obo: ResolvedOboOptions,\n): void {\n    const plan = planGraph(reader, report, options.addMissingNodes, obo);\n    const push = new Pusher(sink, report, options);\n    if (options.restoreMangledIds) {\n        restoreIds(plan.nodes, push.restored);\n    }\n    const namespace = reader.namespaceDefault();\n    // columns, declared only when used, in the vocabulary's order\n    const used = new Set<string>([\"type\"]);\n    for (const record of plan.nodes) {\n        for (const name of [...record.values.keys(), ...record.lists.keys()]) {\n            used.add(name);\n        }\n    }\n    if (namespace !== null) {\n        used.add(\"namespace\");\n    }\n    const columns = new Map<string, ColumnHandle>();\n    for (const name of plan.nodes.length > 0 ? Object.keys(OBO_NODE_COLUMNS) : []) {\n        if (used.has(name)) {\n            columns.set(name, declareResolved(sink, \"node\", oboColumnDecl(\"node\", name), report).handle);\n        }\n    }\n    sink.reserve(plan.nodes.length + plan.placeholders.length, plan.edges.length);\n    for (const record of plan.nodes) {\n        const index = push.node(record.id, record.line);\n        if (index < 0) {\n            continue;\n        }\n        const cells: [string, unknown][] = [[\"type\", record.kind], ...record.values, ...record.lists];\n        if (namespace !== null && !record.values.has(\"namespace\")) {\n            cells.push([\"namespace\", namespace]);\n        }\n        for (const [name, value] of cells) {\n            const handle = columns.get(name);\n            if (handle !== undefined) {\n                sink.setNodeValue(handle, index, value);\n            }\n        }\n    }\n    if (plan.placeholders.length > 0) {\n        const placeholder = declareResolved(sink, \"node\", oboColumnDecl(\"node\", PLACEHOLDER_COLUMN), report).handle;\n        for (const text of plan.placeholders) {\n            const index = push.node(text);\n            if (index >= 0) {\n                sink.setNodeValue(placeholder, index, true);\n            }\n        }\n    }\n    writeEdges(plan, push, options);\n}\n\n/**\n * Take back the ids the exporter rewrote under `sanitizeIds: \"mangle\"`: a frame's\n * `property_value: graphty:originalId \"...\"` names its original id, which replaces the written one\n * wherever the file names it (the property value itself is dropped). An original that another\n * frame already uses as its id is not restored.\n * @param records - the node records\n * @param restored - receives written id to original id\n */\nfunction restoreIds(records: readonly NodeRecord[], restored: Map<string, string>): void {\n    const taken = new Set(records.map((r) => r.id));\n    for (const record of records) {\n        const values = record.lists.get(\"property_value\") as { relation: string; value: string }[] | undefined;\n        const at = values?.findIndex((v) => v.relation === ORIGINAL_ID) ?? -1;\n        if (values === undefined || at < 0) {\n            continue;\n        }\n        const original = originalText(values[at].value);\n        if (taken.has(original)) {\n            continue;\n        }\n        taken.add(original);\n        restored.set(record.id, original);\n        values.splice(at, 1);\n        if (values.length === 0) {\n            record.lists.delete(\"property_value\");\n        }\n    }\n}\n\n/**\n * The original id of a `graphty:originalId` property value: the exporter writes it as JSON text (so\n * every character survives); a value that is not a JSON string is the id as it stands.\n * @param value - the property value\n * @returns the original id\n */\nfunction originalText(value: string): string {\n    try {\n        const parsed: unknown = JSON.parse(value);\n        return typeof parsed === \"string\" ? parsed : value;\n    } catch {\n        return value;\n    }\n}\n\n/**\n * Push the planned edges through the direction resolver, with their relation and qualifiers.\n * @param plan - the plan\n * @param push - the pusher\n * @param options - the resolved options\n */\nfunction writeEdges(plan: GraphPlan, push: Pusher, options: ReturnType<typeof resolveImportOptions>): void {\n    const { sink, report } = push;\n    const direction = new DirectionResolver(sink, report, options.onMixedDirection);\n    direction.setHeader(true);\n    if (plan.edges.length === 0) {\n        return;\n    }\n    const relation = declareResolved(sink, \"edge\", oboColumnDecl(\"edge\", \"relation\"), report).handle;\n    const qualifiers = plan.edges.some((e) => e.edge.qualifiers !== null)\n        ? declareResolved(sink, \"edge\", oboColumnDecl(\"edge\", \"qualifiers\"), report).handle\n        : null;\n    for (const { source, edge } of plan.edges) {\n        push.tick();\n        const before = sink.edgeCount;\n        try {\n            const e = direction.addEdge(push.id(source), push.id(edge.target), \"directed\", undefined, {\n                line: edge.line,\n                element: source,\n            });\n            report.counts.edges += sink.edgeCount - before;\n            if (e < 0) {\n                continue;\n            }\n            sink.setEdgeValue(relation, e, edge.relation);\n            if (qualifiers !== null && edge.qualifiers !== null) {\n                sink.setEdgeValue(qualifiers, e, edge.qualifiers);\n            }\n        } catch (err) {\n            report.recordError(err, { line: edge.line, element: source });\n            report.counts.skippedEdges++;\n        }\n    }\n}\n\n/**\n * Feed the physical lines to the reader as logical lines: backslash continuations joined (the parts\n * collected and joined once, so a value continued over many lines costs its length), form feeds\n * outside quotes split. A backslash inside a `!` comment never continues a line, and a continuation\n * never swallows a frame header or a blank line.\n * @param lines - the line reader\n * @param reader - the OBO reader\n */\nasync function readLines(lines: LineReader, reader: OboReader): Promise<void> {\n    const parts: string[] = [];\n    let partLine = 0;\n    const feed = (text: string, line: number): void => {\n        for (const piece of splitFormFeeds(text)) {\n            reader.line(piece, line);\n        }\n    };\n    for await (const physical of lines) {\n        const { line } = lines;\n        if (parts.length > 0) {\n            const head = physical.trimStart();\n            if (head.length === 0 || head.startsWith(\"[\")) {\n                reader.tally(\n                    \"parse-error\",\n                    OBO_ISSUE.SYNTAX,\n                    \"a line continuation before a frame header or a blank line was ignored\",\n                    \"\\\\\",\n                    partLine,\n                );\n                feed(parts.join(\"\"), partLine);\n                parts.length = 0;\n            } else {\n                reader.tally(\n                    \"coercion\",\n                    OBO_ISSUE.DEPRECATED_SYNTAX,\n                    \"a backslash line continuation was joined (deprecated in 1.4)\",\n                    \"\\\\\",\n                    partLine,\n                );\n            }\n        }\n        if (endsWithContinuation(physical) && stripComment(physical) === physical) {\n            parts.push(physical.slice(0, -1));\n            partLine = line;\n            continue;\n        }\n        if (parts.length > 0) {\n            parts.push(physical);\n            feed(parts.join(\"\"), line);\n            parts.length = 0;\n        } else {\n            feed(physical, line);\n        }\n    }\n    if (parts.length > 0) {\n        reader.tally(\n            \"coercion\",\n            OBO_ISSUE.DEPRECATED_SYNTAX,\n            \"a backslash line continuation was joined (deprecated in 1.4)\",\n            \"\\\\\",\n            partLine,\n        );\n        feed(parts.join(\"\"), partLine);\n    }\n}\n\n/**\n * Confidence that a head is OBO (design 1.5): after a BOM, blank lines and `!` comment lines, 0.9\n * when the first significant line is `format-version:` or a `[Term]` / `[Typedef]` / `[Instance]`\n * header, or such a header follows `tag: value` lines; 0.4 for a head of only `tag: value` lines.\n * @param head - the first bytes\n * @returns the confidence\n */\nfunction sniffObo(head: Uint8Array): number {\n    let text = new TextDecoder(\"utf-8\").decode(head.subarray(0, SNIFF_BYTES));\n    if (text.charCodeAt(0) === 0xfeff) {\n        text = text.slice(1);\n    }\n    const lines = text.split(/\\r\\n|\\r|\\n|\\f/);\n    // the last line may be cut mid-way\n    if (lines.length > 1 && head.byteLength >= SNIFF_BYTES) {\n        lines.pop();\n    }\n    let tagLines = 0;\n    for (const raw of lines) {\n        const line = raw.trim();\n        if (line.length === 0 || line.startsWith(\"!\")) {\n            continue;\n        }\n        if (/^\\[(Term|Typedef|Instance)\\]\\s*(!.*)?$/.test(line)) {\n            return 0.9;\n        }\n        if (tagLines === 0 && /^format-version\\s*:/.test(line)) {\n            return 0.9;\n        }\n        if (/^[A-Za-z][A-Za-z0-9_-]*\\s*:(\\s|$)/.test(line)) {\n            tagLines++;\n            continue;\n        }\n        return 0;\n    }\n    return tagLines > 0 ? 0.4 : 0;\n}\n\n/**\n * The OBO importer plugin.\n * @category Built-in formats\n */\nexport const oboImporter: GraphImporter<OboImportOptions> = Object.freeze({\n    format: \"obo\",\n    options: Object.freeze([\"obsolete\", \"typedefs\"]),\n    extensions: Object.freeze([\".obo\"]),\n    mimeTypes: Object.freeze([\"text/obo\", \"application/obo\"]),\n\n    /**\n     * Confidence that the head is an OBO file.\n     * @param head - the first bytes\n     * @returns the confidence\n     */\n    sniff(head: Uint8Array): number {\n        return sniffObo(head);\n    },\n\n    /**\n     * Read an OBO file into the sink.\n     * @param input - the text, bytes or stream\n     * @param sink - the sink\n     * @param options - format-specific and common options\n     * @returns the import report; ImportError on a fatal error or beyond the error limit\n     */\n    async import(\n        input: ImportInput,\n        sink: GraphSink,\n        options?: OboImportOptions & CommonImportOptions,\n    ): Promise<ImportReport> {\n        const resolved = resolveImportOptions(options, DEFAULTS);\n        const obo = resolveOboOptions(options);\n        const report = new ImportReportBuilder(\"obo\", resolved.errorLimit);\n        reportSinkOptions(sink, options, report, true);\n        reportUnusedOptions(options, report, USED_OPTIONS);\n        const reader = new OboReader(report, resolved.signal, obo.typedefs === \"nodes\");\n        await readLines(new LineReader(input, report, resolved), reader);\n        reader.finishFrame();\n        if (!reader.significant) {\n            report.fail(OBO_ISSUE.EMPTY_INPUT, \"the input is empty\");\n        }\n        const notObo = reader.notObo();\n        if (notObo !== null) {\n            report.fail(\n                OBO_ISSUE.NOT_OBO,\n                `the input is not OBO: it has no frame header and no header tag, and line ${notObo} is not a tag-value line`,\n                { line: notObo },\n            );\n        }\n        throwIfAborted(resolved.signal);\n        reader.checkHeader();\n        writeGraph(reader, sink, report, resolved, obo);\n        const typedefs = ownRecord<Record<string, string[]>>();\n        for (const [id, record] of reader.typedefs) {\n            typedefs[id] = record.raw;\n        }\n        const extra: Record<string, unknown> = { header: reader.headerRecord(), typedefs };\n        if (reader.unknownFrames.length > 0) {\n            extra.unknownFrames = reader.unknownFrames;\n        }\n        sink.setMeta({ ...reader.meta(), extra: { obo: extra } });\n        throwIfAborted(resolved.signal);\n        return report.finish();\n    },\n});\n","/**\n * The OBO exporter: writes a snapshot as an OBO 1.4 flat file, the text format of the Gene\n * Ontology and the OBO Foundry ontologies.\n *\n * Every node is a frame (`[Term]`, or `[Instance]` / `[Typedef]` from the `type` column) in node\n * order; every edge is a clause on its source's frame: `is_a: T` for the relation `is_a`,\n * `instance_of: T` on an Instance, `relationship: R T` for anything else, an edge without a\n * relation as `is_a` (the `relation` option). The columns of the OBO vocabulary\n * (src/common/ontology.ts: `name`, `namespace`, `def`, `synonym`, `xref`, ...) are written back\n * as their tags; any other node column becomes `property_value: <column> \"<value>\" xsd:<type>`\n * lines (with a `[Typedef]` declaring the column as a metadata relation), any other edge column a\n * qualifier of the edge's clause. A placeholder node (`graphty.placeholder`, a target no frame\n * declared) gets no frame, so the re-import makes it again. The header, the Typedefs and the\n * unknown frames an OBO import kept in `meta.extra.obo` are written back.\n *\n * check() predicts every difference the OBO importer produces on re-import: a vocabulary column\n * whose values the file cannot carry exactly is written as `property_value` lines instead and\n * reported, never written half right.\n */\n\nimport { type Column, GraphFormatError, type GraphSnapshot, type NodeId } from \"@graphty/graph-format\";\n\nimport {\n    COLUMN_AS_PROPERTY_VALUE_CODE,\n    GRAPH_COLUMN_AS_METADATA_CODE,\n    NODE_ORDER_CODE,\n    RELATION_ASSUMED_CODE,\n    ROLE_ASSUMED_CODE,\n    TYPEDEF_NODES_CODE,\n} from \"../../common/codes.js\";\nimport { type PairFolding, pairFolding } from \"../../common/direction.js\";\nimport { capabilities, LOSS } from \"../../common/export.js\";\nimport { formatNumber } from \"../../common/format.js\";\nimport { OBO_NODE_COLUMNS, PLACEHOLDER_COLUMN, SYNONYM_SCOPES } from \"../../common/ontology.js\";\nimport {\n    capabilityNotes,\n    cellOf,\n    emptyColumnNotes,\n    fitsVocabulary,\n    FRAME_KINDS,\n    type FrameKind,\n    framelessNodes,\n    isQualifierRecord,\n    movedNodes,\n    type NoteFn,\n    notePropertyColumn,\n    slotColumn,\n    textOf,\n    UNWRITTEN_ROLES,\n} from \"../../common/ontology-export.js\";\nimport { type ResolvedExportOptions, resolveExportOptions } from \"../../common/options.js\";\nimport { agree, plural } from \"../../common/plural.js\";\nimport { type ExplicitWeights, explicitWeights } from \"../../common/weights.js\";\nimport { encodeChunks, joinText } from \"../../common/writer.js\";\nimport { type CommonExportOptions, type ExportCapabilities, type GraphExporter, type LossNote } from \"../../types.js\";\nimport { BOOL_TAGS, DEPRECATED_TAGS, ID_LIST_TAGS, TEXT_TAGS, TYPEDEF_TAGS } from \"./importer.js\";\nimport {\n    escapeOboQuoted,\n    escapeOboValue,\n    escapeOboWord,\n    hasLineEnd,\n    isOboWord,\n    isQualifierName,\n    NOT_IN_WORD,\n    qualifierBlock,\n    tokenize,\n} from \"./syntax.js\";\n\n/**\n * The format-specific options of the OBO exporter.\n * @category Built-in formats\n */\nexport interface OboExportOptions extends CommonExportOptions {\n    /**\n     * The relation written for an edge that has none of its own (no `relation` value): an OBO id\n     * such as `is_a` or `part_of`. Reasoners and ROBOT read `is_a` as subclassing.\n     * @defaultValue \"is_a\"\n     */\n    relation?: string | undefined;\n    /**\n     * The `ontology` id written in the header, such as `go` or `uberon`. It may hold letters,\n     * digits and `_ . - /`; any other character makes checkExport() and the save throw\n     * E_UNSUPPORTED. The default is the id an OBO import read, else the graph name with every other\n     * character replaced by `_`, else no `ontology` line.\n     * @defaultValue as read, else the graph name\n     */\n    ontology?: string | undefined;\n}\n\n/**\n * The loss notes the OBO exporter's check() returns, by name. A key is the code without its\n * severity and format prefixes.\n * @category Built-in formats\n */\nexport const OBO_LOSS = Object.freeze({\n    /** A node column outside the OBO vocabulary (or one whose values a tag cannot carry exactly) reads back inside the `property_value` column. */\n    COLUMN_AS_PROPERTY_VALUE: COLUMN_AS_PROPERTY_VALUE_CODE,\n    /** An edge column (or the explicit weights) reads back inside the `qualifiers` column. */\n    EDGE_COLUMN_AS_QUALIFIER: \"W_OBO_EDGE_COLUMN_AS_QUALIFIER\",\n    /** Every edge is written from its source to its target, so an undirected graph reads back as directed. */\n    UNDIRECTED_AS_DIRECTED: \"W_OBO_UNDIRECTED_AS_DIRECTED\",\n    /** Two identical clauses on one frame (parallel edges with one relation and the same qualifiers, a repeated list item) read back as one. */\n    DUPLICATE_CLAUSE: \"W_OBO_DUPLICATE_CLAUSE\",\n    /** An edge without a relation is written with the `relation` option (default `is_a`). */\n    RELATION_ASSUMED: RELATION_ASSUMED_CODE,\n    /** A relation that is not an OBO id (empty, or holding a space, `!`, `{` or `}`) is written with `_` in place of those characters. */\n    RELATION_RENAMED: \"W_OBO_RELATION_RENAMED\",\n    /** The graph name is not an ontology id; the header `ontology` is written with `_` in place of the other characters. */\n    ONTOLOGY_NAME: \"W_OBO_ONTOLOGY_NAME\",\n    /** `[Typedef]` frames read back as nodes only under the importer's `typedefs: \"nodes\"`; by default they are metadata. */\n    TYPEDEF_NODES: TYPEDEF_NODES_CODE,\n    /** Edges are written in the frame of their source node, so they read back grouped by source, in node order. */\n    EDGE_ORDER: \"W_OBO_EDGE_ORDER\",\n    /**\n     * A graph attribute is written as a header `property_value` and reads back in `snapshot.meta.extra.obo.header`,\n     * not as a graph attribute.\n     */\n    GRAPH_COLUMN_AS_METADATA: GRAPH_COLUMN_AS_METADATA_CODE,\n    /** A carriage return or form feed in a text cannot be written; it is written as a line feed. */\n    LINE_END: \"W_OBO_LINE_END\",\n    /** The nodes read back in a different order. */\n    NODE_ORDER: NODE_ORDER_CODE,\n    /** A mutual pair is written as two clauses without its mark. */\n    MUTUAL_EXPANDED: LOSS.MUTUAL_EXPANDED,\n    /**\n     * The undirected edges of a mixed graph are written the way `onMixedDirection` chose (\"directed\" or \"undirected\").\n     */\n    MIXED_DIRECTION: LOSS.MIXED_DIRECTION,\n    /**\n     * The graph has both directed and undirected edges and `onMixedDirection` is \"error\". An import stops; a save to a\n     * format that holds one direction per file fails with E_DIRECTED. Pass \"directed\" or \"undirected\" to read or write\n     * it anyway.\n     */\n    MIXED_DIRECTION_ERROR: LOSS.MIXED_DIRECTION_ERROR,\n    /** OBO has no edge ids. */\n    EDGE_IDS_DROPPED: LOSS.EDGE_IDS_DROPPED,\n    /** OBO has no positions. */\n    POSITIONS_DROPPED: LOSS.POSITIONS,\n    /** OBO has no containment. */\n    HIERARCHY_DROPPED: LOSS.HIERARCHY,\n    /** OBO has no time. */\n    TEMPORAL_DROPPED: LOSS.TEMPORAL,\n    /** OBO has no visual columns. */\n    VIZ_DROPPED: LOSS.VIZ,\n    /** An attribute with a role the format has no place for is written as a plain attribute; the role is lost. */\n    ROLE_DROPPED: LOSS.ROLE,\n    /**\n     * An attribute without a role is written where the format keeps a role (for example, a `name` column as the label), and\n     * reads back with that role.\n     */\n    ROLE_ASSUMED: ROLE_ASSUMED_CODE,\n    /**\n     * An attribute with a role (for example, the label) is written where the format keeps that role, and reads back under the\n     * name the format's importer gives it.\n     */\n    COLUMN_NAME_CHANGED: LOSS.COLUMN_NAME_CHANGED,\n    /**\n     * An OBO attribute stored as text where graph-io uses a dictionary (or the other way round); it reads back with\n     * graph-io's usual type. The values are the same.\n     */\n    DTYPE_UNSUPPORTED: LOSS.DTYPE,\n    /** A column without a value on any written element reads back absent. */\n    EMPTY_COLUMN_DROPPED: LOSS.EMPTY_COLUMN,\n    /** A declared default: OBO has none. */\n    DEFAULT_DROPPED: LOSS.DEFAULT,\n    /** Declared options: OBO has no enumerations. */\n    OPTIONS_DROPPED: LOSS.OPTIONS,\n    /** An extension table OBO cannot carry. */\n    EXTENSION_TABLE_DROPPED: LOSS.EXTENSION_TABLE,\n    /**\n     * Node ids the format cannot write, under `sanitizeIds: \"error\"`; the save fails with E_INVALID_ID. Pass\n     * `sanitizeIds: \"mangle\"` to rewrite them.\n     */\n    ID_CHARSET: LOSS.ID_CHARSET,\n    /** Node ids OBO cannot write as they are, under sanitizeIds \"mangle\": rewritten, the original kept. */\n    ID_MANGLED: LOSS.ID_MANGLED,\n    /** Numeric ids are written as text and read back as strings. */\n    ID_TEXT_TYPE: LOSS.ID_TEXT_TYPE,\n    /**\n     * Two node ids would be written as the same text (the number 5 and the text \"5\"); the save fails with\n     * E_INVALID_ID.\n     */\n    ID_TEXT_COLLISION: LOSS.ID_TEXT_COLLISION,\n});\n\n/**\n * What the OBO flat file keeps: a directed multigraph with self-loops and any id (the exporter's\n * own rule refuses whitespace, control characters, `!`, `{` and `}`). No column of the snapshot's own reads back as\n * a column: the file keeps the OBO vocabulary (`name`, `def`, `synonym`, ... with their own\n * types) and writes every other node column as property values and every edge column as\n * qualifiers, which check() reports column by column.\n * @category Built-in formats\n */\nexport const OBO_CAPABILITIES: ExportCapabilities = capabilities({\n    mixedDirection: false,\n    multiEdges: true,\n    selfLoops: true,\n    edgeIds: \"none\",\n    idCharset: \"any\",\n    dtypes: [],\n    components: false,\n    lists: false,\n    json: false,\n    defaults: false,\n    options: false,\n    hierarchy: false,\n    temporal: \"none\",\n    graphAttributes: false,\n    positions: false,\n    viz: false,\n});\n\n/** The roles OBO has a slot for, and the column names its importer gives them. */\n\n/** The node column that keeps a rewritten id's original (restored by restoreMangledIds). */\nconst ORIGINAL_ID = \"graphty:originalId\";\n\n/** The edge columns of the vocabulary. */\nconst RELATION_COLUMN = \"relation\";\nconst QUALIFIERS_COLUMN = \"qualifiers\";\n\n/** The qualifier name the explicit weights are written under. */\nconst WEIGHT_QUALIFIER = \"weight\";\n\n/** The relations a file may use without declaring them (the importer's built-ins). */\nconst BUILTIN_RELATIONS: ReadonlySet<string> = new Set([\n    \"is_a\",\n    \"instance_of\",\n    \"disjoint_from\",\n    \"inverse_of\",\n    \"union_of\",\n    \"intersection_of\",\n]);\n\n/** Marks where the edge clauses go in TAG_ORDER. */\nconst EDGES = \"\\u0000edges\";\n\n/** Marks where the unknown tags go in TAG_ORDER. */\nconst UNRECOGNIZED = \"obo.unrecognized\";\n\n/** The order of the tags in a frame (the OBO 1.4 guide's, Term, Instance and Typedef tags merged). */\nconst TAG_ORDER: readonly string[] = [\n    \"is_anonymous\",\n    \"name\",\n    \"namespace\",\n    \"alt_id\",\n    \"def\",\n    \"comment\",\n    \"subset\",\n    \"synonym\",\n    \"xref\",\n    \"builtin\",\n    \"property_value\",\n    \"domain\",\n    \"range\",\n    \"holds_over_chain\",\n    \"is_anti_symmetric\",\n    \"is_cyclic\",\n    \"is_reflexive\",\n    \"is_symmetric\",\n    \"is_asymmetric\",\n    \"is_transitive\",\n    \"is_functional\",\n    \"is_inverse_functional\",\n    EDGES,\n    \"intersection_of\",\n    \"union_of\",\n    \"equivalent_to\",\n    \"disjoint_from\",\n    \"inverse_of\",\n    \"transitive_over\",\n    \"equivalent_to_chain\",\n    \"disjoint_over\",\n    \"created_by\",\n    \"creation_date\",\n    \"is_obsolete\",\n    \"replaced_by\",\n    \"consider\",\n    \"expand_assertion_to\",\n    \"expand_expression_to\",\n    \"is_metadata_tag\",\n    \"is_class_level\",\n    UNRECOGNIZED,\n];\n\n/** The header tags in the 1.4 guide's order; every other kept header tag follows them. */\nconst HEADER_ORDER: readonly string[] = [\n    \"format-version\",\n    \"data-version\",\n    \"version\",\n    \"date\",\n    \"saved-by\",\n    \"auto-generated-by\",\n    \"import\",\n    \"subsetdef\",\n    \"synonymtypedef\",\n    \"idspace\",\n    \"default-relationship-id-prefix\",\n    \"id-mapping\",\n    \"default-namespace\",\n    \"namespace-id-rule\",\n    \"remark\",\n    \"ontology\",\n];\n\n/** Tags the importer applies (so an unknown tag of that name would not read back as unknown). */\nconst APPLIED_TAGS: ReadonlySet<string> = new Set([\n    \"id\",\n    \"is_a\",\n    \"instance_of\",\n    \"relationship\",\n    \"intersection_of\",\n    \"holds_over_chain\",\n    \"equivalent_to_chain\",\n    \"def\",\n    \"expand_assertion_to\",\n    \"expand_expression_to\",\n    \"synonym\",\n    \"xref\",\n    \"property_value\",\n    ...TEXT_TAGS,\n    ...BOOL_TAGS,\n    ...ID_LIST_TAGS,\n    ...DEPRECATED_TAGS.keys(),\n]);\n\n/** The vocabulary node columns the flat file writes as tags (`type`, `name` and `propertyType` aside). */\nconst TAG_COLUMNS: ReadonlySet<string> = new Set(\n    Object.keys(OBO_NODE_COLUMNS).filter((name) => name !== \"type\" && name !== \"name\" && name !== \"propertyType\"),\n);\n\n/** The xsd datatype of a dtype in a `property_value` line. */\nconst XSD: Readonly<Record<string, string>> = Object.freeze({\n    string: \"xsd:string\",\n    dict: \"xsd:string\",\n    bool: \"xsd:boolean\",\n    i32: \"xsd:integer\",\n    u32: \"xsd:integer\",\n    u8: \"xsd:integer\",\n    f32: \"xsd:double\",\n    f64: \"xsd:double\",\n});\n\n/** A node column written as `property_value` lines. */\ninterface PropertyColumn {\n    readonly column: Column;\n    /** The relation the lines name (the column name, or its id form). */\n    readonly relation: string;\n}\n\n/** An edge column written as qualifiers. */\ninterface QualifierColumn {\n    readonly column: Column;\n    /** The qualifier name (the column name, or its written form). */\n    readonly name: string;\n}\n\n/** Everything write() needs, computed once by plan(). */\ninterface Plan {\n    readonly notes: LossNote[];\n    readonly fatal: GraphFormatError | null;\n    readonly options: { readonly relation: string; readonly ontology: string | null };\n    /** The id written for each node. */\n    readonly ids: readonly string[];\n    /** The rewritten nodes' original ids, by node index. */\n    readonly originals: ReadonlyMap<number, string>;\n    /** 1 for a node written without a frame (a placeholder the re-import makes again). */\n    readonly frameless: Uint8Array;\n    /** The frame type of each node. */\n    readonly kinds: readonly FrameKind[];\n    /** The label column (written as `name`), or null. */\n    readonly label: Column | null;\n    /** The vocabulary columns written as their tags, by tag. */\n    readonly tags: ReadonlyMap<string, Column>;\n    /** The node columns written as `property_value` lines. */\n    readonly properties: readonly PropertyColumn[];\n    /** The written edges by source: edgeStart[i]..edgeStart[i + 1] in edgeOrder. */\n    readonly edgeStart: Uint32Array;\n    readonly edgeOrder: Uint32Array;\n    /** The target of each edge. */\n    readonly dst: ArrayLike<number>;\n    /** The relation written for each edge. */\n    readonly relations: readonly string[];\n    /** The vocabulary `qualifiers` edge column, or null. */\n    readonly qualifiers: Column | null;\n    /** The other edge columns written as qualifiers. */\n    readonly edgeColumns: readonly QualifierColumn[];\n    readonly weights: ExplicitWeights;\n    /** The header lines. */\n    readonly header: readonly string[];\n    /** The frames after the nodes (kept Typedefs, declared relations, unknown frames), as lines. */\n    readonly tail: readonly string[];\n}\n\n/** Counts gathered while frames are written. */\ninterface FrameStats {\n    /** Texts holding a carriage return or form feed. */\n    lineEnds: number;\n    /** Whether every `obo.qualifiers` entry found its clause. */\n    qualifiersPlaced: boolean;\n}\n\n// ============================================================ values\n\n/**\n * Whether a text survives as an unquoted tag value: the reader trims it, and the OBO grammar\n * (fastobo, owlapi) refuses an empty one.\n * @param text - the text\n * @returns true when the text is not empty and has no surrounding whitespace\n */\nfunction isTrimmed(text: string): boolean {\n    return text.length > 0 && text === text.trim();\n}\n\n/**\n * Whether a value is an array whose items all pass a test.\n * @param value - the value\n * @param item - the item test\n * @param nonEmpty - whether the array must have an item\n * @returns true when it is such an array\n */\nfunction arrayOf(value: unknown, item: (v: unknown) => boolean, nonEmpty = true): value is unknown[] {\n    return Array.isArray(value) && (!nonEmpty || value.length > 0) && value.every(item);\n}\n\n/**\n * Whether a value is a string the unquoted xref slot keeps (non-empty, no surrounding whitespace).\n * @param value - the value\n * @returns true for such a string\n */\nfunction isXrefId(value: unknown): value is string {\n    return typeof value === \"string\" && value.length > 0 && isTrimmed(value);\n}\n\n/**\n * Whether a value is an OBO word.\n * @param value - the value\n * @returns true for a string isOboWord() accepts\n */\nfunction isWord(value: unknown): value is string {\n    return typeof value === \"string\" && isOboWord(value);\n}\n\n/**\n * Whether an object has exactly the given keys, `qualifiers` optional (and then a qualifier record).\n * @param value - the value\n * @param keys - the required keys\n * @returns true when it has those keys and nothing else\n */\nfunction hasKeys(value: unknown, keys: readonly string[]): value is Record<string, unknown> {\n    if (typeof value !== \"object\" || value === null || Array.isArray(value)) {\n        return false;\n    }\n    const own = Object.keys(value);\n    const record = value as Record<string, unknown>;\n    if (Object.hasOwn(record, \"qualifiers\")) {\n        if (!isQualifierRecord(record.qualifiers, isQualifierName)) {\n            return false;\n        }\n        return own.length === keys.length + 1 && keys.every((k) => Object.hasOwn(record, k));\n    }\n    return own.length === keys.length && keys.every((k) => Object.hasOwn(record, k));\n}\n\n/**\n * Replace every character a word cannot hold with `_`.\n * @param text - the text\n * @returns a word\n */\nfunction wordOf(text: string): string {\n    const out = text.replaceAll(new RegExp(NOT_IN_WORD.source, \"gu\"), \"_\");\n    return out.length === 0 ? \"_\" : out;\n}\n\n/**\n * A qualifier record as name / value pairs (a list value as one pair per item).\n * @param record - a record isQualifierRecord() accepts\n * @returns the pairs\n */\nfunction qualifierPairs(record: unknown): [string, string][] {\n    const out: [string, string][] = [];\n    for (const [name, value] of Object.entries(record as Record<string, string | string[]>)) {\n        for (const item of Array.isArray(value) ? value : [value]) {\n            out.push([name, item]);\n        }\n    }\n    return out;\n}\n\n// ============================================================ the plan\n\n/**\n * Resolve the OBO-specific options.\n * @param options - the caller's options\n * @returns the relation and the ontology; E_UNSUPPORTED for a value that is not an OBO id\n */\nfunction resolveOboOptions(options: OboExportOptions | undefined): {\n    readonly relation: string;\n    readonly ontology: string | null;\n} {\n    const relation = options?.relation ?? \"is_a\";\n    if (typeof relation !== \"string\" || !isOboWord(relation)) {\n        throw new GraphFormatError(\"E_UNSUPPORTED\", `option relation: ${JSON.stringify(relation)} is not an OBO id`, {\n            option: \"relation\",\n            found: relation,\n        });\n    }\n    const ontology = options?.ontology ?? null;\n    if (ontology !== null && (typeof ontology !== \"string\" || !/^[A-Za-z0-9_.\\-/]+$/.test(ontology))) {\n        throw new GraphFormatError(\n            \"E_UNSUPPORTED\",\n            `option ontology: ${JSON.stringify(ontology)} is not an ontology id (letters, digits, _ . - /)`,\n            { option: \"ontology\", found: ontology },\n        );\n    }\n    return { relation, ontology };\n}\n\n/**\n * The ids to write: each node's id text, or under \"mangle\" a word with `_` for the characters a\n * word cannot hold (and `_2`, `_3`... on a collision), the original kept.\n * @param snapshot - the snapshot\n * @param mode - the sanitizeIds option\n * @param note - records a note\n * @returns the ids, the originals and the fatal error, if any\n */\nfunction planIds(\n    snapshot: GraphSnapshot,\n    mode: \"error\" | \"mangle\",\n    note: NoteFn,\n): { ids: string[]; originals: Map<number, string>; fatal: GraphFormatError | null } {\n    const n = snapshot.nodeCount;\n    const ids: string[] = new Array<string>(n);\n    const bad: number[] = [];\n    let numeric = 0;\n    for (let i = 0; i < n; i++) {\n        const id: NodeId = snapshot.ids.idOf(i);\n        if (typeof id === \"number\") {\n            numeric++;\n        }\n        ids[i] = String(id);\n        if (!isOboWord(ids[i])) {\n            bad.push(i);\n        }\n    }\n    if (numeric > 0) {\n        note(\n            LOSS.ID_TEXT_TYPE,\n            `${numeric} numeric node id${plural(numeric)} ${agree(numeric, \"is\", \"are\")} written as text and read back as strings`,\n            null,\n            numeric,\n        );\n    }\n    const originals = new Map<number, string>();\n    let fatal: GraphFormatError | null = null;\n    if (bad.length > 0 && mode === \"error\") {\n        fatal = refuseIds(snapshot, ids, bad, note);\n    } else if (bad.length > 0) {\n        mangleIds(ids, bad, originals, note);\n    }\n    return { ids, originals, fatal: fatal ?? collidingIds(snapshot, ids, note) };\n}\n\n/**\n * Note the ids that are not OBO words, for a save that refuses them.\n * @param snapshot - the snapshot\n * @param ids - the id texts\n * @param bad - the indices of the ids that are not OBO words\n * @param note - records a note\n * @returns the error the save throws\n */\nfunction refuseIds(\n    snapshot: GraphSnapshot,\n    ids: readonly string[],\n    bad: readonly number[],\n    note: NoteFn,\n): GraphFormatError {\n    note(\n        LOSS.ID_CHARSET,\n        `${bad.length} node id${plural(bad.length)} ${agree(bad.length, \"is\", \"are\")} not OBO ids (empty, or holding whitespace, a control character, \"!\", \"{\" or \"}\"); the save fails unless sanitizeIds is \"mangle\"`,\n        null,\n        bad.length,\n    );\n    return new GraphFormatError(\n        \"E_INVALID_ID\",\n        `${bad.length} node id${plural(bad.length)} cannot be written as OBO ids (first: ${JSON.stringify(ids[bad[0]])}); pass sanitizeIds: \"mangle\" to rewrite them`,\n        { reason: \"charset\", count: bad.length, id: snapshot.ids.idOf(bad[0]), index: bad[0] },\n    );\n}\n\n/**\n * Rewrite the ids that are not OBO words with \"_\" (and `_2`, `_3`... on a collision), keeping the\n * originals.\n * @param ids - the id texts, rewritten in place\n * @param bad - the indices of the ids that are not OBO words\n * @param originals - receives each rewritten id's original text\n * @param note - records a note\n */\nfunction mangleIds(ids: string[], bad: readonly number[], originals: Map<number, string>, note: NoteFn): void {\n    const badSet = new Set(bad);\n    const used = new Set(ids.filter((_, i) => !badSet.has(i)));\n    for (const i of bad) {\n        const base = wordOf(ids[i]);\n        let candidate = base;\n        let k = 2;\n        while (used.has(candidate)) {\n            candidate = `${base}_${k}`;\n            k++;\n        }\n        used.add(candidate);\n        originals.set(i, ids[i]);\n        ids[i] = candidate;\n    }\n    note(\n        LOSS.ID_MANGLED,\n        `${bad.length} node id${plural(bad.length)} that ${agree(bad.length, \"is\", \"are\")} not OBO ids ${agree(bad.length, \"is\", \"are\")} rewritten with \"_\"; the originals are kept as ${ORIGINAL_ID} property values (JSON text; an import with restoreMangledIds: true reads them back as the ids)`,\n        null,\n        bad.length,\n    );\n}\n\n/**\n * Note the first two node ids that have the same text, which OBO cannot tell apart.\n * @param snapshot - the snapshot\n * @param ids - the id texts\n * @param note - records a note\n * @returns the error the save throws, or null when every text is unique\n */\nfunction collidingIds(snapshot: GraphSnapshot, ids: readonly string[], note: NoteFn): GraphFormatError | null {\n    const seen = new Map<string, number>();\n    for (let i = 0; i < ids.length; i++) {\n        const before = seen.get(ids[i]);\n        if (before !== undefined) {\n            note(\n                LOSS.ID_TEXT_COLLISION,\n                `node ids ${JSON.stringify(snapshot.ids.idOf(before))} and ${JSON.stringify(snapshot.ids.idOf(i))} have the same text; the save fails`,\n                null,\n                1,\n            );\n            return new GraphFormatError(\"E_INVALID_ID\", \"two node ids have the same text; OBO keeps ids as text\", {\n                reason: \"collision\",\n            });\n        }\n        seen.set(ids[i], i);\n    }\n    return null;\n}\n\n/**\n * The written edges (the mirror halves of folded pairs left out) grouped by source, in node order\n * then edge order, and the direction notes.\n * @param snapshot - the snapshot\n * @param folding - the pair folding\n * @param common - the common options\n * @param note - records a note\n * @returns the edge list, the CSR by source and the targets\n */\nfunction planEdges(\n    snapshot: GraphSnapshot,\n    folding: PairFolding,\n    common: ResolvedExportOptions,\n    note: NoteFn,\n): { written: number[]; edgeStart: Uint32Array; edgeOrder: Uint32Array; dst: ArrayLike<number> } {\n    const { src, dst } = snapshot.edgeList();\n    const written: number[] = [];\n    for (let e = 0; e < snapshot.edgeCount; e++) {\n        if (!folding.folded(e)) {\n            written.push(e);\n        }\n    }\n    const edgeStart = new Uint32Array(snapshot.nodeCount + 1);\n    for (const e of written) {\n        edgeStart[src[e] + 1]++;\n    }\n    for (let i = 0; i < snapshot.nodeCount; i++) {\n        edgeStart[i + 1] += edgeStart[i];\n    }\n    const fill = edgeStart.slice(0, snapshot.nodeCount);\n    const edgeOrder = new Uint32Array(written.length);\n    for (const e of written) {\n        edgeOrder[fill[src[e]]++] = e;\n    }\n    let moved = 0;\n    for (let k = 0; k < edgeOrder.length; k++) {\n        if (edgeOrder[k] !== written[k]) {\n            moved++;\n        }\n    }\n    if (moved > 0) {\n        note(\n            OBO_LOSS.EDGE_ORDER,\n            `${moved} edge${plural(moved)} ${agree(moved, \"reads\", \"read\")} back at another position: edges are written on their source's frame, grouped by source in node order`,\n            null,\n            moved,\n        );\n    }\n    if (!snapshot.directed) {\n        note(\n            OBO_LOSS.UNDIRECTED_AS_DIRECTED,\n            `the snapshot is undirected; every edge is written from its source to its target and reads back directed (${written.length} edge${plural(written.length)})`,\n            null,\n            written.length,\n        );\n    } else if (common.onMixedDirection !== \"error\") {\n        const undirected = written.filter((e) => !folding.sourceDirected(e)).length;\n        if (undirected > 0) {\n            note(\n                OBO_LOSS.UNDIRECTED_AS_DIRECTED,\n                `${undirected} undirected edge${plural(undirected)} ${agree(undirected, \"is\", \"are\")} written as one directed clause each; OBO has no undirected edge`,\n                null,\n                undirected,\n            );\n        }\n    }\n    if (folding.mutualCount > 0) {\n        note(\n            LOSS.MUTUAL_EXPANDED,\n            `${folding.mutualCount} mutual pair${plural(folding.mutualCount)} ${agree(folding.mutualCount, \"is\", \"are\")} written as two clauses; the mutual mark is lost`,\n            null,\n            folding.mutualCount,\n        );\n    }\n    return { written, edgeStart, edgeOrder, dst };\n}\n\n/**\n * The frame types: the `type` column when every written node has one of Term, Instance or\n * Typedef, else Term for every node (and the column is a property value).\n * @param snapshot - the snapshot\n * @param frameless - the frameless flags\n * @returns the kinds and the type column used, or null\n */\nfunction planKinds(snapshot: GraphSnapshot, frameless: Uint8Array): { kinds: FrameKind[]; type: Column | null } {\n    const kinds = new Array<FrameKind>(snapshot.nodeCount).fill(\"Term\");\n    const type = snapshot.nodes.get(\"type\");\n    if (type === null || (type.dtype !== \"dict\" && type.dtype !== \"string\")) {\n        return { kinds, type: null };\n    }\n    for (let i = 0; i < snapshot.nodeCount; i++) {\n        if (frameless[i] === 1) {\n            if (type.isSet(i)) {\n                return { kinds: kinds.fill(\"Term\"), type: null };\n            }\n            continue;\n        }\n        const value = cellOf(type, i);\n        if (typeof value !== \"string\" || !FRAME_KINDS.has(value)) {\n            return { kinds: kinds.fill(\"Term\"), type: null };\n        }\n        kinds[i] = value as FrameKind;\n    }\n    return { kinds, type };\n}\n\n/**\n * Whether a vocabulary column's values are written by its tag and read back unchanged, on every\n * written node (the vocabulary's dtype, the shape the importer builds, OBO words where the tag\n * takes an id, no surrounding space in an unquoted value, a Typedef tag on Typedef frames only).\n * @param name - the column (a TAG_COLUMNS name)\n * @param column - the column\n * @param rows - the written nodes\n * @param kinds - the frame types\n * @param scopes - the default scope of each declared synonym type\n * @returns true when the tag carries the column\n */\nfunction tagCarries(\n    name: string,\n    column: Column,\n    rows: readonly number[],\n    kinds: readonly FrameKind[],\n    scopes: ReadonlyMap<string, string | null>,\n): boolean {\n    const spec = OBO_NODE_COLUMNS[name];\n    if (!fitsVocabulary(spec.dtype, column) || column.meta.components > 1) {\n        return false;\n    }\n    const typedefOnly = TYPEDEF_TAGS.has(name);\n    const valid = (v: unknown): boolean => {\n        if (TEXT_TAGS.has(name)) {\n            return typeof v === \"string\" && isTrimmed(v);\n        }\n        if (BOOL_TAGS.has(name)) {\n            return typeof v === \"boolean\";\n        }\n        if (ID_LIST_TAGS.has(name)) {\n            return arrayOf(v, isWord);\n        }\n        switch (name) {\n            case \"def\":\n                return typeof v === \"string\";\n            case \"def.xrefs\":\n                return arrayOf(v, isXrefId, false);\n            case \"xref\":\n                return arrayOf(v, isXrefId);\n            case \"xref.descriptions\":\n                return (\n                    typeof v === \"object\" &&\n                    v !== null &&\n                    !Array.isArray(v) &&\n                    Object.values(v).every((d) => typeof d === \"string\")\n                );\n            case \"synonym\":\n                return arrayOf(\n                    v,\n                    (s) =>\n                        hasKeys(s, [\"text\", \"scope\", \"type\", \"xrefs\"]) &&\n                        typeof s.text === \"string\" &&\n                        typeof s.scope === \"string\" &&\n                        SYNONYM_SCOPES.has(s.scope) &&\n                        (s.type === null || isWord(s.type)) &&\n                        (s.type === null || (scopes.get(s.type) ?? s.scope) === s.scope) &&\n                        arrayOf(s.xrefs, isXrefId, false),\n                );\n            case \"intersection_of\":\n                return arrayOf(\n                    v,\n                    (x) =>\n                        hasKeys(x, [\"relation\", \"target\"]) &&\n                        (x.relation === null || isWord(x.relation)) &&\n                        isWord(x.target),\n                );\n            case \"property_value\":\n                return arrayOf(\n                    v,\n                    (x) =>\n                        hasKeys(x, [\"relation\", \"value\", \"datatype\"]) &&\n                        isWord(x.relation) &&\n                        x.relation !== ORIGINAL_ID &&\n                        typeof x.value === \"string\" &&\n                        (x.datatype === null || isWord(x.datatype)),\n                );\n            case \"holds_over_chain\":\n            case \"equivalent_to_chain\":\n                return arrayOf(v, (pair) => arrayOf(pair, isWord) && pair.length === 2);\n            case \"expand_assertion_to\":\n            case \"expand_expression_to\":\n                return arrayOf(\n                    v,\n                    (x) =>\n                        hasKeys(x, [\"template\", \"xrefs\"]) &&\n                        typeof x.template === \"string\" &&\n                        arrayOf(x.xrefs, isXrefId, false),\n                );\n            case \"obo.qualifiers\":\n                return (\n                    typeof v === \"object\" &&\n                    v !== null &&\n                    !Array.isArray(v) &&\n                    Object.values(v).every((entries) =>\n                        arrayOf(\n                            entries,\n                            (entry) =>\n                                hasKeys(entry, [\"value\"]) &&\n                                Object.hasOwn(entry, \"qualifiers\") &&\n                                typeof entry.value === \"string\" &&\n                                isQualifierRecord(entry.qualifiers, isQualifierName),\n                        ),\n                    )\n                );\n            default:\n                return false;\n        }\n    };\n    for (const i of rows) {\n        if (!column.isSet(i)) {\n            continue;\n        }\n        if (typedefOnly && kinds[i] !== \"Typedef\") {\n            return false;\n        }\n        if (!valid(cellOf(column, i))) {\n            return false;\n        }\n    }\n    return true;\n}\n\n/**\n * Whether the `obo.unrecognized` column reads back unchanged: a record of tag to texts, each tag\n * one the importer does not apply on that frame type.\n * @param column - the column\n * @param rows - the written nodes\n * @param kinds - the frame types\n * @returns true when every cell is written as unknown tags and read back as the same\n */\nfunction unrecognizedCarried(column: Column, rows: readonly number[], kinds: readonly FrameKind[]): boolean {\n    if (column.dtype !== \"json\") {\n        return false;\n    }\n    for (const i of rows) {\n        const v = cellOf(column, i);\n        if (v === undefined) {\n            continue;\n        }\n        if (typeof v !== \"object\" || v === null || Array.isArray(v)) {\n            return false;\n        }\n        for (const [tag, values] of Object.entries(v)) {\n            const applied =\n                (APPLIED_TAGS.has(tag) || TYPEDEF_TAGS.has(tag)) &&\n                !(TYPEDEF_TAGS.has(tag) && kinds[i] !== \"Typedef\") &&\n                !(tag === \"instance_of\" && kinds[i] !== \"Instance\");\n            if (\n                applied ||\n                tag.length === 0 ||\n                !isTrimmed(tag) ||\n                !arrayOf(values, (t) => typeof t === \"string\" && isTrimmed(t))\n            ) {\n                return false;\n            }\n        }\n    }\n    return true;\n}\n\n/**\n * The default scope of each synonym type the kept header declares (null: none declared).\n * @param header - the kept header (tag to raw values)\n * @returns the scopes by type\n */\nfunction synonymTypeScopes(header: Readonly<Record<string, readonly string[]>>): Map<string, string | null> {\n    const out = new Map<string, string | null>();\n    for (const raw of header.synonymtypedef ?? []) {\n        const tokens = tokenize(raw);\n        if (tokens.length > 0 && tokens[0].kind === \"word\") {\n            const scope = tokens.slice(1).find((t) => t.kind === \"word\" && SYNONYM_SCOPES.has(t.text));\n            out.set(tokens[0].text, scope?.text ?? null);\n        }\n    }\n    return out;\n}\n\n/**\n * The record of an OBO import kept under `meta.extra.obo`, or empty records.\n * @param snapshot - the snapshot\n * @returns the header, the Typedefs and the unknown frames\n */\nfunction keptObo(snapshot: GraphSnapshot): {\n    header: Record<string, string[]>;\n    typedefs: Record<string, Record<string, string[]>>;\n    unknownFrames: { type: string; clauses: Record<string, string[]> }[];\n} {\n    const raw = snapshot.meta.extra.obo;\n    const record =\n        typeof raw === \"object\" && raw !== null && !Array.isArray(raw) ? (raw as Record<string, unknown>) : {};\n    const clauses = (value: unknown): Record<string, string[]> => {\n        const out: Record<string, string[]> = {};\n        if (typeof value === \"object\" && value !== null && !Array.isArray(value)) {\n            for (const [tag, values] of Object.entries(value)) {\n                if (Array.isArray(values)) {\n                    out[tag] = values.filter((v): v is string => typeof v === \"string\");\n                }\n            }\n        }\n        return out;\n    };\n    const typedefs: Record<string, Record<string, string[]>> = {};\n    if (typeof record.typedefs === \"object\" && record.typedefs !== null && !Array.isArray(record.typedefs)) {\n        for (const [id, frame] of Object.entries(record.typedefs)) {\n            typedefs[id] = clauses(frame);\n        }\n    }\n    const unknownFrames = Array.isArray(record.unknownFrames)\n        ? record.unknownFrames.flatMap((f: unknown) =>\n              typeof f === \"object\" && f !== null && typeof (f as { type?: unknown }).type === \"string\"\n                  ? [{ type: (f as { type: string }).type, clauses: clauses((f as { clauses?: unknown }).clauses) }]\n                  : [],\n          )\n        : [];\n    return { header: clauses(record.header), typedefs, unknownFrames };\n}\n\n/**\n * Plan an export: the notes, the fatal condition and what is written.\n * @param snapshot - the snapshot\n * @param options - the caller's options\n * @returns the plan\n */\nfunction plan(snapshot: GraphSnapshot, options: (OboExportOptions & CommonExportOptions) | undefined): Plan {\n    const common = resolveExportOptions(options);\n    const obo = resolveOboOptions(options);\n    const notes: LossNote[] = [];\n    const note: NoteFn = (code, message, column = null, count = null) => {\n        notes.push(Object.freeze({ code, message, column, count }));\n    };\n    let fatal: GraphFormatError | null = null;\n\n    const { ids, originals, fatal: idFatal } = planIds(snapshot, common.sanitizeIds, note);\n    fatal ??= idFatal;\n    const folding = pairFolding(snapshot);\n    const { written, edgeStart, edgeOrder, dst } = planEdges(snapshot, folding, common, note);\n    const frameless = framelessNodes(snapshot, written, {\n        outgoingAllowed: false,\n        changed: (i) => originals.has(i),\n    });\n    const moved = movedNodes(\n        frameless,\n        Array.from(edgeOrder, (e) => dst[e]),\n    );\n    if (moved > 0) {\n        note(\n            NODE_ORDER_CODE,\n            `${moved} node${plural(moved)} ${agree(moved, \"reads\", \"read\")} back at another position: placeholder nodes have no frame and read back after the written nodes`,\n            null,\n            moved,\n        );\n    }\n    const rows: number[] = [];\n    for (let i = 0; i < snapshot.nodeCount; i++) {\n        if (frameless[i] === 0) {\n            rows.push(i);\n        }\n    }\n    const { kinds, type } = planKinds(snapshot, frameless);\n    const typedefNodes = rows.filter((i) => kinds[i] === \"Typedef\").length;\n    if (typedefNodes > 0) {\n        note(\n            OBO_LOSS.TYPEDEF_NODES,\n            `${typedefNodes} node${plural(typedefNodes)} ${agree(typedefNodes, \"is\", \"are\")} written as [Typedef] frames; they read back as nodes only when imported with typedefs: \"nodes\", and then after the other nodes, with the [Typedef] frames that declare the relations`,\n            \"type\",\n            typedefNodes,\n        );\n    }\n\n    const kept = keptObo(snapshot);\n    const scopes = synonymTypeScopes(kept.header);\n    // the label: the label column, or a role-less name column\n    const labelSlot = slotColumn(snapshot.nodes, \"label\", \"name\");\n    const labelColumn = labelSlot.column;\n    const label =\n        labelColumn !== null && rows.every((i) => !labelColumn.isSet(i) || isTrimmed(String(labelColumn.value(i))))\n            ? labelColumn\n            : null;\n    const tags = planTags(snapshot, rows, kinds, scopes, label);\n    fatal ??= capabilityNotes(snapshot, common, {\n        caps: OBO_CAPABILITIES,\n        label,\n        labelAssumed: labelSlot.assumed,\n        edgeSlot: \"a qualifier\",\n        note,\n    });\n    oboColumnNotes(snapshot, label, tags, note);\n    const properties = planProperties(snapshot, rows, frameless, label, tags, type, note);\n\n    // edges\n    const relationSlot = slotColumn(snapshot.edges, \"kind\", RELATION_COLUMN);\n    const relations = planRelations(snapshot, written, relationSlot.column, obo.relation, note);\n    if (relationSlot.assumed && relationSlot.column !== null) {\n        note(\n            ROLE_ASSUMED_CODE,\n            `edge column \"${RELATION_COLUMN}\" has no role, so it is taken as the relation of each edge: it is written as each line's relation, and reads back with the relation role (\"kind\")`,\n            RELATION_COLUMN,\n            relationSlot.column.length - relationSlot.column.nullCount,\n        );\n    }\n    const weights = explicitWeights(snapshot);\n    const { qualifiers, edgeColumns } = planEdgeColumns(snapshot, written, relationSlot.column, weights, note);\n    emptyColumnNotes(snapshot, rows, frameless, written, note);\n\n    const p: Plan = {\n        notes,\n        fatal,\n        options: obo,\n        ids,\n        originals,\n        frameless,\n        kinds,\n        label,\n        tags,\n        properties,\n        edgeStart,\n        edgeOrder,\n        dst,\n        relations,\n        qualifiers,\n        edgeColumns,\n        weights,\n        header: [],\n        tail: [],\n    };\n    // write every frame once: the duplicate clauses, the line ends and the qualifier placement\n    let stats = simulate(p, rows);\n    if (!stats.qualifiersPlaced) {\n        tags.delete(\"obo.qualifiers\");\n        const column = snapshot.nodes.get(\"obo.qualifiers\");\n        if (column !== null) {\n            properties.push({ column, relation: \"obo.qualifiers\" });\n            notePropertyColumn(note, column, rows, \"property_value lines (relation obo.qualifiers)\");\n        }\n        stats = simulate(p, rows);\n    }\n    if (stats.duplicates > 0) {\n        note(\n            OBO_LOSS.DUPLICATE_CLAUSE,\n            `${stats.duplicates} clause${plural(stats.duplicates)} ${agree(stats.duplicates, \"repeats\", \"repeat\")} another clause of their frame word for word (parallel edges with one relation and the same qualifiers, a repeated list item) and read back as one`,\n            null,\n            stats.duplicates,\n        );\n    }\n    const header = planHeader(snapshot, kept.header, obo, rows, tags, note, stats);\n    const tail = planTail({\n        kept,\n        rows,\n        kinds,\n        ids,\n        properties,\n        relations,\n        edges: edgeOrder,\n        xref: tags.get(\"xref\") ?? null,\n    });\n    if (stats.lineEnds > 0) {\n        note(\n            OBO_LOSS.LINE_END,\n            `${stats.lineEnds} text${plural(stats.lineEnds)} ${agree(stats.lineEnds, \"holds\", \"hold\")} a carriage return or form feed, which OBO cannot carry; written as a line feed`,\n            null,\n            stats.lineEnds,\n        );\n    }\n    return { ...p, header, tail };\n}\n\n/**\n * The vocabulary columns written as their tags: each one tagCarries() accepts, then the pairs\n * resolved (def.xrefs needs def, a def needs its def.xrefs written when that column exists, the\n * xref descriptions need their xrefs written).\n * @param snapshot - the snapshot\n * @param rows - the written nodes\n * @param kinds - the frame types\n * @param scopes - the default scope of each declared synonym type\n * @param label - the label column (never a tag)\n * @returns the columns by tag\n */\nfunction planTags(\n    snapshot: GraphSnapshot,\n    rows: readonly number[],\n    kinds: readonly FrameKind[],\n    scopes: ReadonlyMap<string, string | null>,\n    label: Column | null,\n): Map<string, Column> {\n    const tags = new Map<string, Column>();\n    for (const name of TAG_COLUMNS) {\n        const column = snapshot.nodes.get(name);\n        if (column === null || column === label || (column.meta.role !== null && column.meta.role !== \"label\")) {\n            continue;\n        }\n        if (\n            name === UNRECOGNIZED\n                ? unrecognizedCarried(column, rows, kinds)\n                : tagCarries(name, column, rows, kinds, scopes)\n        ) {\n            tags.set(name, column);\n        }\n    }\n    // pairs: def.xrefs needs def; xref.descriptions needs its xrefs written\n    const def = tags.get(\"def\");\n    const defXrefs = tags.get(\"def.xrefs\");\n    if (defXrefs !== undefined && (def === undefined || rows.some((i) => def.isSet(i) !== defXrefs.isSet(i)))) {\n        tags.delete(\"def.xrefs\");\n    }\n    if (def !== undefined && !tags.has(\"def.xrefs\") && snapshot.nodes.get(\"def.xrefs\") !== null) {\n        // a def.xrefs column that is not written would read back as the empty list on every def\n        tags.delete(\"def\");\n    }\n    const descriptions = tags.get(\"xref.descriptions\");\n    if (descriptions !== undefined && !rows.every((i) => describedXrefsWritten(tags, descriptions, i))) {\n        tags.delete(\"xref.descriptions\");\n    }\n\n    return tags;\n}\n\n/**\n * Whether every described xref of a node is written in one of its xref slots (so the description\n * has a place).\n * @param tags - the columns written as tags\n * @param descriptions - the `xref.descriptions` column\n * @param row - the node\n * @returns true when every description has its xref\n */\nfunction describedXrefsWritten(tags: ReadonlyMap<string, Column>, descriptions: Column, row: number): boolean {\n    const map = cellOf(descriptions, row) as Record<string, string> | undefined;\n    if (map === undefined) {\n        return true;\n    }\n    const written = new Set<string>();\n    const add = (values: unknown): void => {\n        if (Array.isArray(values)) {\n            for (const v of values) {\n                if (typeof v === \"string\") {\n                    written.add(v);\n                }\n            }\n        }\n    };\n    for (const name of [\"def.xrefs\", \"xref\"]) {\n        const column = tags.get(name);\n        if (column !== undefined) {\n            add(cellOf(column, row));\n        }\n    }\n    for (const name of [\"synonym\", \"expand_assertion_to\", \"expand_expression_to\"]) {\n        const column = tags.get(name);\n        const items = column === undefined ? undefined : cellOf(column, row);\n        if (Array.isArray(items)) {\n            for (const item of items as { xrefs: unknown }[]) {\n                add(item.xrefs);\n            }\n        }\n    }\n    return Object.keys(map).every((id) => written.has(id));\n}\n\n/**\n * The OBO-only column notes: the vocabulary column of the other text dtype, and the graph columns\n * written as header property values.\n * @param snapshot - the snapshot\n * @param label - the label column written as `name`, or null\n * @param tags - the vocabulary columns written as tags\n * @param note - records a note\n */\nfunction oboColumnNotes(\n    snapshot: GraphSnapshot,\n    label: Column | null,\n    tags: ReadonlyMap<string, Column>,\n    note: NoteFn,\n): void {\n    for (const [name, column] of [...tags, ...(label === null ? [] : ([[\"name\", label]] as const))]) {\n        const want = name === \"name\" ? \"string\" : OBO_NODE_COLUMNS[name].dtype;\n        if (\n            ((want === \"string\" || want === \"dict\") && column.dtype !== want) ||\n            (column.dtype === \"list\" && column.child.dtype !== \"string\")\n        ) {\n            const held = column.dtype === \"list\" ? `${column.child.dtype} items` : column.dtype;\n            note(\n                LOSS.DTYPE,\n                `node column \"${column.meta.name}\" holds ${held}; it reads back as ${column.dtype === \"list\" ? \"string items\" : want}`,\n                column.meta.name,\n                column.length - column.nullCount,\n            );\n        }\n    }\n    for (const column of snapshot.graph) {\n        note(\n            GRAPH_COLUMN_AS_METADATA_CODE,\n            `graph column \"${column.meta.name}\" is written as a header property_value and reads back in meta.extra.obo.header, not as a column`,\n            column.meta.name,\n            column.length - column.nullCount,\n        );\n    }\n}\n\n/**\n * The node columns written as `property_value` lines: every column that is not written by a tag,\n * the label or the type, and not one OBO leaves out (positions, visual and temporal columns), each\n * with its note.\n * @param snapshot - the snapshot\n * @param rows - the written nodes\n * @param frameless - the frameless flags\n * @param label - the label column\n * @param tags - the columns written as tags\n * @param type - the type column\n * @param note - records a note\n * @returns the columns\n */\nfunction planProperties(\n    snapshot: GraphSnapshot,\n    rows: readonly number[],\n    frameless: Uint8Array,\n    label: Column | null,\n    tags: ReadonlyMap<string, Column>,\n    type: Column | null,\n    note: NoteFn,\n): PropertyColumn[] {\n    const out: PropertyColumn[] = [];\n    const slotted = new Set<Column>([\n        ...tags.values(),\n        ...(label === null ? [] : [label]),\n        ...(type === null ? [] : [type]),\n    ]);\n    for (const column of snapshot.nodes) {\n        const { role, name } = column.meta;\n        if (slotted.has(column) || (role !== null && UNWRITTEN_ROLES.has(role))) {\n            continue;\n        }\n        if (name === PLACEHOLDER_COLUMN && rows.every((i) => !column.isSet(i)) && frameless.includes(1)) {\n            // read back from the frameless nodes alone\n            continue;\n        }\n        const relation = isOboWord(name) && name !== ORIGINAL_ID ? name : wordOf(name.replaceAll(\":\", \"_\"));\n        out.push({ column, relation });\n        notePropertyColumn(note, column, rows, `property_value lines (relation ${relation})`);\n    }\n    return out;\n}\n\n/**\n * The relation written for each edge, with the notes of the assumed and renamed ones.\n * @param snapshot - the snapshot\n * @param written - the written edges\n * @param relation - the relation column, or null\n * @param fallback - the relation of an edge without one\n * @param note - records a note\n * @returns the relation per edge index\n */\nfunction planRelations(\n    snapshot: GraphSnapshot,\n    written: readonly number[],\n    relation: Column | null,\n    fallback: string,\n    note: NoteFn,\n): string[] {\n    const out = new Array<string>(snapshot.edgeCount).fill(fallback);\n    let assumed = 0;\n    let renamed = 0;\n    for (const e of written) {\n        const value = relation === null ? undefined : cellOf(relation, e);\n        if (typeof value !== \"string\") {\n            assumed++;\n            continue;\n        }\n        if (isOboWord(value)) {\n            out[e] = value;\n        } else {\n            out[e] = wordOf(value);\n            renamed++;\n        }\n    }\n    if (assumed > 0) {\n        note(\n            OBO_LOSS.RELATION_ASSUMED,\n            `${assumed} edge${plural(assumed)} ${agree(assumed, \"has\", \"have\")} no relation; written as ${fallback} (an ontology reads is_a as subclassing)`,\n            relation?.meta.name ?? null,\n            assumed,\n        );\n    }\n    if (renamed > 0) {\n        note(\n            OBO_LOSS.RELATION_RENAMED,\n            `${renamed} relation${plural(renamed)} ${agree(renamed, \"is\", \"are\")} not OBO ids; written with \"_\" in place of the space, \"!\", \"{\" or \"}\"`,\n            relation?.meta.name ?? null,\n            renamed,\n        );\n    }\n    return out;\n}\n\n/**\n * The edge columns written as qualifiers: the vocabulary `qualifiers` column when its cells are\n * qualifier records, every other edge column (and the explicit weights) as `name=\"value\"` pairs,\n * each with its note.\n * @param snapshot - the snapshot\n * @param written - the written edges\n * @param relation - the relation column\n * @param weights - the explicit weights\n * @param note - records a note\n * @returns the qualifiers column and the other columns\n */\nfunction planEdgeColumns(\n    snapshot: GraphSnapshot,\n    written: readonly number[],\n    relation: Column | null,\n    weights: ExplicitWeights,\n    note: NoteFn,\n): { qualifiers: Column | null; edgeColumns: QualifierColumn[] } {\n    const qualifiers = qualifierRecords(snapshot, written);\n    const edgeColumns: QualifierColumn[] = [];\n    const count = (column: Column): number => written.filter((e) => column.isSet(e)).length;\n    const merged = qualifiers === null ? \"\" : \" (merged with its values)\";\n    for (const column of snapshot.edges) {\n        const { role, name } = column.meta;\n        if (\n            column === relation ||\n            column === qualifiers ||\n            role === \"id\" ||\n            (role !== null && UNWRITTEN_ROLES.has(role))\n        ) {\n            continue;\n        }\n        const written2 = isQualifierName(name) ? name : wordOf(name.replaceAll(/[=\",[\\]\\\\]/g, \"_\"));\n        edgeColumns.push({ column, name: written2 });\n        const n = count(column);\n        if (n > 0) {\n            note(\n                OBO_LOSS.EDGE_COLUMN_AS_QUALIFIER,\n                `edge column \"${name}\" is written as the qualifier ${written2} and reads back inside the qualifiers column${merged}`,\n                name,\n                n,\n            );\n        }\n    }\n    const explicit = weights.weighted ? written.filter((e) => weights.isExplicit(e)).length : 0;\n    if (explicit > 0) {\n        note(\n            OBO_LOSS.EDGE_COLUMN_AS_QUALIFIER,\n            `${explicit} explicit edge weight${plural(explicit)} ${agree(explicit, \"is\", \"are\")} written as the qualifier ${WEIGHT_QUALIFIER} and read back inside the qualifiers column, not as weights`,\n            snapshot.edges.byRole(\"weight\")?.meta.name ?? null,\n            explicit,\n        );\n    }\n    return { qualifiers, edgeColumns };\n}\n\n/**\n * The vocabulary `qualifiers` edge column, when every written cell of it is a qualifier record.\n * @param snapshot - the snapshot\n * @param written - the written edges\n * @returns the column, or null when there is none or it holds something else\n */\nfunction qualifierRecords(snapshot: GraphSnapshot, written: readonly number[]): Column | null {\n    const qualifiers = snapshot.edges.get(QUALIFIERS_COLUMN);\n    if (qualifiers?.dtype !== \"json\" || qualifiers.meta.role !== null) {\n        return null;\n    }\n    const records = written.every(\n        (e) => !qualifiers.isSet(e) || isQualifierRecord(cellOf(qualifiers, e), isQualifierName),\n    );\n    return records ? qualifiers : null;\n}\n\n/**\n * The header lines: the kept header in the guide's order with the missing fields filled from the\n * metadata, and the graph columns as `property_value` lines.\n * @param snapshot - the snapshot\n * @param kept - the kept header\n * @param obo - the OBO options\n * @param obo.ontology - the ontology option, or null\n * @param rows - the written nodes\n * @param tags - the columns written as tags\n * @param note - records a note\n * @param stats - the line-end counter\n * @returns the lines\n */\nfunction planHeader(\n    snapshot: GraphSnapshot,\n    kept: Readonly<Record<string, readonly string[]>>,\n    obo: { readonly ontology: string | null },\n    rows: readonly number[],\n    tags: ReadonlyMap<string, Column>,\n    note: NoteFn,\n    stats: FrameStats,\n): string[] {\n    const { values, filled } = headerFields(snapshot, kept, obo.ontology, note);\n    // a default namespace applies to every frame without one: keep it only when none lacks one\n    const namespace = tags.get(\"namespace\");\n    if (values.has(\"default-namespace\") && (namespace === undefined || rows.some((i) => !namespace.isSet(i)))) {\n        values.delete(\"default-namespace\");\n    }\n    const lines: string[] = [];\n    // the filled fields in the guide's order, then the kept ones as the file had them\n    const tagsInOrder = [\n        ...HEADER_ORDER.filter((t) => filled.has(t)),\n        ...[...values.keys()].filter((t) => !filled.has(t)),\n    ];\n    for (const tag of tagsInOrder) {\n        for (const value of values.get(tag) ?? []) {\n            lines.push(`${escapeTag(tag)}: ${value}`);\n        }\n    }\n    if (lines.length === 0 && rows.length === 0) {\n        // a file of nothing reads back as an empty input: the version line makes it an empty ontology\n        lines.push(\"format-version: 1.4\");\n    }\n    for (const column of snapshot.graph) {\n        const relation = isOboWord(column.meta.name) ? column.meta.name : wordOf(column.meta.name);\n        for (const line of propertyLines({ column, relation }, 0, stats)) {\n            lines.push(`property_value: ${line}`);\n        }\n    }\n    return lines;\n}\n\n/**\n * The header fields: the kept ones, and for a graph not read from OBO the fields its metadata has.\n * @param snapshot - the snapshot\n * @param kept - the kept header\n * @param ontologyOption - the ontology option, or null\n * @param note - records a note\n * @returns the values by tag, and the tags filled in (not kept)\n */\nfunction headerFields(\n    snapshot: GraphSnapshot,\n    kept: Readonly<Record<string, readonly string[]>>,\n    ontologyOption: string | null,\n    note: NoteFn,\n): { values: Map<string, string[]>; filled: Set<string> } {\n    const { meta } = snapshot;\n    const values = new Map<string, string[]>(Object.entries(kept).map(([tag, v]) => [tag, v.map(rawValue)]));\n    const filled = new Set<string>();\n    const fill = (tag: string, value: string | null): void => {\n        if (value !== null && !values.has(tag)) {\n            values.set(tag, [value]);\n            filled.add(tag);\n        }\n    };\n    // a file read from OBO keeps its own header; any other graph gets the fields its metadata has\n    if (meta.sourceFormat !== \"obo\") {\n        fill(\"format-version\", \"1.4\");\n        fill(\"date\", oboDate(meta.created));\n        fill(\"saved-by\", meta.creator === null ? null : escapeOboValue(meta.creator));\n    }\n    const ontology = ontologyField(ontologyOption, meta.name, values.has(\"ontology\"), note);\n    if (ontology !== null) {\n        if (!values.has(\"ontology\")) {\n            filled.add(\"ontology\");\n        }\n        values.set(\"ontology\", [ontology]);\n    }\n    return { values, filled };\n}\n\n/**\n * The ontology header field to write: the ontology option, else the graph name when it is an\n * ontology id, else the name rewritten with \"_\" when the kept header has none.\n * @param option - the ontology option, or null\n * @param name - the graph name, or null\n * @param kept - whether the kept header has an ontology field\n * @param note - records a note\n * @returns the value to set, or null to leave the field as it is\n */\nfunction ontologyField(option: string | null, name: string | null, kept: boolean, note: NoteFn): string | null {\n    if (option !== null) {\n        return option;\n    }\n    if (name === null || name.length === 0 || kept) {\n        return null;\n    }\n    if (/^[A-Za-z0-9_.\\-/]+$/.test(name)) {\n        return name;\n    }\n    const slug = name.replaceAll(/[^A-Za-z0-9_.-]/g, \"_\");\n    note(\n        OBO_LOSS.ONTOLOGY_NAME,\n        `the graph name ${JSON.stringify(name)} is not an ontology id; written as ${slug}`,\n        null,\n        null,\n    );\n    return slug;\n}\n\n/**\n * A kept raw value made safe for one line (a line break in metadata a caller built becomes `\\n`).\n * @param raw - the raw value\n * @returns the value to write\n */\nfunction rawValue(raw: string): string {\n    return raw.replaceAll(/\\r\\n|\\r|\\n|\\f/g, String.raw`\\n`);\n}\n\n/**\n * A tag name escaped for the left of its colon.\n * @param tag - the tag\n * @returns the escaped tag\n */\nfunction escapeTag(tag: string): string {\n    return escapeOboValue(tag).replaceAll(\":\", String.raw`\\:`);\n}\n\n/**\n * An ISO date (`yyyy-MM-ddTHH:mm...`) as the OBO header date `dd:MM:yyyy HH:mm`.\n * @param iso - the date, or null\n * @returns the header text, or null when the date is not of that form\n */\nfunction oboDate(iso: string | null): string | null {\n    const m = iso === null ? null : /^(\\d{4})-(\\d{2})-(\\d{2})(?:T(\\d{2}):(\\d{2}))?/.exec(iso);\n    if (m === null) {\n        return null;\n    }\n    return `${m[3]}:${m[2]}:${m[1]} ${m[4] ?? \"00\"}:${m[5] ?? \"00\"}`;\n}\n\n/** What the frames after the nodes are planned from. */\ninterface TailInput {\n    /** The kept Typedef frames and unknown frames. */\n    readonly kept: {\n        typedefs: Record<string, Record<string, string[]>>;\n        unknownFrames: { type: string; clauses: Record<string, string[]> }[];\n    };\n    /** The written nodes. */\n    readonly rows: readonly number[];\n    /** The frame type of each node. */\n    readonly kinds: readonly FrameKind[];\n    /** The written id of each node. */\n    readonly ids: readonly string[];\n    /** The property-value columns. */\n    readonly properties: readonly PropertyColumn[];\n    /** The relation of each edge. */\n    readonly relations: readonly string[];\n    /** The written edges. */\n    readonly edges: Iterable<number>;\n    /** The xref column written as tags (a Typedef node's xrefs declare relations), or null. */\n    readonly xref: Column | null;\n}\n\n/**\n * The frames after the nodes: the kept Typedefs (unless a node is that Typedef), a declaration of\n * every relation and property-value relation no Typedef declares, and the kept unknown frames.\n * @param input - what the frames are planned from\n * @returns the lines\n */\nfunction planTail(input: TailInput): string[] {\n    const { kept, rows, properties, relations } = input;\n    const lines: string[] = [];\n    const declared = nodeTypedefs(input);\n    keptTypedefLines(kept.typedefs, declared, lines);\n    const declare = (relation: string, metadata: boolean): void => {\n        if (declared.has(relation)) {\n            return;\n        }\n        declared.add(relation);\n        lines.push(\"\", \"[Typedef]\", `id: ${escapeOboWord(relation)}`, `name: ${escapeOboValue(relation)}`);\n        if (metadata) {\n            lines.push(\"is_metadata_tag: true\");\n        }\n    };\n    const used = new Set<string>();\n    for (const e of input.edges) {\n        used.add(relations[e]);\n    }\n    for (const { column, relation } of properties) {\n        if (rows.some((i) => column.isSet(i))) {\n            declare(relation, true);\n        }\n    }\n    for (const relation of used) {\n        declare(relation, false);\n    }\n    for (const frame of kept.unknownFrames) {\n        lines.push(\"\", `[${frame.type.replaceAll(/[\\]\\r\\n]/g, \"_\")}]`, ...clauseLines(frame.clauses));\n    }\n    return lines;\n}\n\n/**\n * The relations the built-in ones, the Typedef nodes and their xrefs declare.\n * @param input - what the frames are planned from\n * @returns the declared relation ids\n */\nfunction nodeTypedefs(input: TailInput): Set<string> {\n    const { rows, kinds, ids, xref } = input;\n    const declared = new Set<string>(BUILTIN_RELATIONS);\n    for (const i of rows) {\n        if (kinds[i] !== \"Typedef\") {\n            continue;\n        }\n        declared.add(ids[i]);\n        const xrefs = xref === null ? undefined : cellOf(xref, i);\n        for (const x of Array.isArray(xrefs) ? xrefs : []) {\n            declared.add(String(x));\n        }\n    }\n    return declared;\n}\n\n/**\n * Write the kept Typedef frames no node already declares, and declare them and their xrefs.\n * @param typedefs - the kept Typedef frames by id\n * @param declared - the declared relations, added to\n * @param lines - the lines, appended to\n */\nfunction keptTypedefLines(\n    typedefs: Record<string, Record<string, string[]>>,\n    declared: Set<string>,\n    lines: string[],\n): void {\n    for (const [id, clauses] of Object.entries(typedefs)) {\n        if (declared.has(id) && !BUILTIN_RELATIONS.has(id)) {\n            continue;\n        }\n        declared.add(id);\n        lines.push(\"\", \"[Typedef]\", `id: ${escapeOboWord(id)}`, ...clauseLines(clauses, \"id\"));\n        for (const xref of clauses.xref ?? []) {\n            declared.add(xref.trim());\n        }\n    }\n}\n\n/**\n * The clause lines of a kept frame, each value made safe for one line.\n * @param clauses - the values by tag\n * @param skip - a tag to leave out, or null\n * @returns the lines\n */\nfunction clauseLines(clauses: Record<string, string[]>, skip: string | null = null): string[] {\n    return Object.entries(clauses)\n        .filter(([tag]) => tag !== skip)\n        .flatMap(([tag, values]) => values.map((value) => `${escapeTag(tag)}: ${rawValue(value)}`));\n}\n\n// ============================================================ the frames\n\n/** Hands out the `obo.qualifiers` entries of one frame to the clauses they belong to, in order. */\nclass QualifierCursor {\n    private readonly entries: Record<string, { value: string; qualifiers: unknown }[]>;\n\n    private readonly next = new Map<string, number>();\n\n    /**\n     * Create a cursor.\n     * @param cell - the frame's `obo.qualifiers` cell, or undefined\n     */\n    constructor(cell: unknown) {\n        this.entries = (cell ?? {}) as Record<string, { value: string; qualifiers: unknown }[]>;\n    }\n\n    /**\n     * The qualifier block of a clause: the next entry of its tag when that entry is for this value.\n     * @param tag - the tag (or `<tag>.xrefs` for an xref inside a list)\n     * @param value - the clause's value as the column holds it\n     * @returns the block with a leading space, or \"\"\n     */\n    block(tag: string, value: string): string {\n        const list = Object.hasOwn(this.entries, tag) ? this.entries[tag] : undefined;\n        const k = this.next.get(tag) ?? 0;\n        if (list === undefined || k >= list.length || list[k].value !== value) {\n            return \"\";\n        }\n        this.next.set(tag, k + 1);\n        return qualifierBlock(qualifierPairs(list[k].qualifiers));\n    }\n\n    /**\n     * Whether every entry found its clause.\n     * @returns true when all were placed\n     */\n    placed(): boolean {\n        return Object.entries(this.entries).every(([tag, list]) => (this.next.get(tag) ?? 0) === list.length);\n    }\n}\n\n/** The per-frame writer state. */\ninterface FrameState {\n    readonly p: Plan;\n    readonly row: number;\n    readonly cursor: QualifierCursor;\n    /** The xrefs whose description was written already. */\n    readonly described: Set<string>;\n    readonly stats: FrameStats;\n}\n\n/**\n * Count a text that loses a line end, and return it.\n * @param s - the frame state's stats\n * @param text - the text\n * @returns the text\n */\nfunction counted(s: FrameStats, text: string): string {\n    if (hasLineEnd(text)) {\n        s.lineEnds++;\n    }\n    return text;\n}\n\n/**\n * One xref as written inside a list or after `xref:`: its id, its description the first time the\n * frame names it, and its own qualifiers.\n * @param f - the frame state\n * @param id - the xref id\n * @param listTag - the `<tag>.xrefs` key of its qualifiers, or null after `xref:`\n * @returns the text\n */\nfunction xrefText(f: FrameState, id: string, listTag: string | null): string {\n    let out = escapeOboValue(counted(f.stats, id));\n    const descriptions = f.p.tags.get(\"xref.descriptions\");\n    const map =\n        descriptions === undefined ? undefined : (cellOf(descriptions, f.row) as Record<string, string> | undefined);\n    if (map !== undefined && Object.hasOwn(map, id) && !f.described.has(id)) {\n        f.described.add(id);\n        out += ` \"${escapeOboQuoted(counted(f.stats, map[id]))}\"`;\n    }\n    if (listTag !== null) {\n        out += f.cursor.block(listTag, id);\n    }\n    return out;\n}\n\n/**\n * An xref list: `[A:1, B:2 \"description\"]`.\n * @param f - the frame state\n * @param ids - the xref ids\n * @param tag - the clause's tag\n * @returns the list\n */\nfunction xrefList(f: FrameState, ids: readonly string[], tag: string): string {\n    const field = `${tag}.xrefs`;\n    return `[${ids.map((id) => xrefText(f, id, field)).join(\", \")}]`;\n}\n\n/**\n * The `property_value` values of one cell of a property column: `relation \"value\" xsd:type` per\n * value (a list item each, JSON text for nested values).\n * @param prop - the column and its relation\n * @param row - the row\n * @param stats - the line-end counter\n * @returns the values after `property_value: `\n */\nfunction propertyLines(prop: PropertyColumn, row: number, stats: FrameStats): string[] {\n    const { column, relation } = prop;\n    const value = cellOf(column, row);\n    if (value === undefined) {\n        return [];\n    }\n    const head = escapeOboWord(relation);\n    const one = (v: unknown, dtype: string): string => {\n        let text: string;\n        let xsd = XSD[dtype] ?? \"xsd:string\";\n        if (typeof v === \"number\" && xsd === \"xsd:double\") {\n            text = xsdDouble(v, dtype);\n        } else if (typeof v === \"string\" || typeof v === \"boolean\" || typeof v === \"number\") {\n            text = textOf(v, dtype);\n        } else {\n            text = JSON.stringify(v) ?? \"null\";\n            xsd = \"xsd:string\";\n        }\n        return `${head} \"${escapeOboQuoted(counted(stats, text))}\" ${xsd}`;\n    };\n    if (column.dtype === \"list\") {\n        return (value as readonly unknown[]).map((item) => one(item, column.child.dtype));\n    }\n    if (column.dtype === \"json\" || column.meta.components > 1) {\n        return [one(value, \"json\")];\n    }\n    return [one(value, column.dtype)];\n}\n\n/**\n * A double as xsd:double writes it: INF, -INF and NaN for the non-finite values.\n * @param v - the value\n * @param dtype - the column dtype (f32 values use their shortest text)\n * @returns the text\n */\nfunction xsdDouble(v: number, dtype: string): string {\n    if (Number.isNaN(v)) {\n        return \"NaN\";\n    }\n    if (!Number.isFinite(v)) {\n        return v > 0 ? \"INF\" : \"-INF\";\n    }\n    return formatNumber(v, dtype === \"f32\" ? \"f32\" : \"f64\");\n}\n\n/**\n * The qualifier block of one edge: the `qualifiers` record, then the other columns and the weight.\n * @param f - the frame state\n * @param e - the edge\n * @returns the block with a leading space, or \"\"\n */\nfunction edgeQualifiers(f: FrameState, e: number): string {\n    const { p } = f;\n    const pairs: [string, string][] = [];\n    if (p.qualifiers !== null) {\n        const record = cellOf(p.qualifiers, e);\n        if (record !== undefined) {\n            pairs.push(...qualifierPairs(record));\n        }\n    }\n    for (const { column, name } of p.edgeColumns) {\n        pairs.push(...qualifierTexts(column, e).map((text): [string, string] => [name, text]));\n    }\n    const weight = p.weights.text(e);\n    if (weight !== null) {\n        pairs.push([WEIGHT_QUALIFIER, weight]);\n    }\n    for (const [, value] of pairs) {\n        counted(f.stats, value);\n    }\n    return qualifierBlock(pairs);\n}\n\n/**\n * The qualifier values an edge column gives one edge: one per item of a list, none when unset.\n * @param column - the edge column\n * @param e - the edge\n * @returns the value texts\n */\nfunction qualifierTexts(column: Column, e: number): string[] {\n    const value = cellOf(column, e);\n    if (value === undefined) {\n        return [];\n    }\n    if (column.dtype === \"list\") {\n        return (value as readonly unknown[]).map((item) => textOf(item, column.child.dtype));\n    }\n    return [column.dtype === \"json\" ? (JSON.stringify(value) ?? \"null\") : textOf(value, column.dtype)];\n}\n\n/**\n * The clauses of one tag column on a frame.\n * @param f - the frame state\n * @param tag - the tag\n * @param column - the column\n * @param out - the lines\n */\nfunction tagLines(f: FrameState, tag: string, column: Column, out: string[]): void {\n    const value = cellOf(column, f.row);\n    if (value === undefined) {\n        return;\n    }\n    const { cursor, stats } = f;\n    const push = (text: string, stored: string, raw = false): void => {\n        out.push(`${tag}: ${raw ? text : escapeOboValue(counted(stats, text))}${cursor.block(tag, stored)}`);\n    };\n    if (TEXT_TAGS.has(tag)) {\n        push(value as string, value as string);\n        return;\n    }\n    if (BOOL_TAGS.has(tag)) {\n        push(value ? \"true\" : \"false\", value ? \"true\" : \"false\", true);\n        return;\n    }\n    if (ID_LIST_TAGS.has(tag)) {\n        for (const id of value as string[]) {\n            push(escapeOboWord(id), id, true);\n        }\n        return;\n    }\n    // def.xrefs, xref.descriptions and obo.qualifiers are written with the clauses they belong to\n    if (Object.hasOwn(STRUCTURED_TAGS, tag)) {\n        STRUCTURED_TAGS[tag](f, tag, value, out);\n    }\n}\n\n/** Writes the clauses of a structured tag column's cell. */\ntype StructuredLines = (f: FrameState, tag: string, value: unknown, out: string[]) => void;\n\n/**\n * The qualifier block of a structured value.\n * @param qualifiers - the value's qualifiers, or undefined\n * @returns the block with a leading space, or \"\"\n */\nfunction blockOf(qualifiers: unknown): string {\n    return qualifiers === undefined ? \"\" : qualifierBlock(qualifierPairs(qualifiers));\n}\n\n/** The writers of the tags whose cells hold more than a text, an id list or a boolean. */\nconst STRUCTURED_TAGS: Readonly<Record<string, StructuredLines>> = {\n    def(f, _tag, value, out) {\n        const xrefs = f.p.tags.get(\"def.xrefs\");\n        const ids = (xrefs === undefined ? [] : (cellOf(xrefs, f.row) ?? [])) as string[];\n        const text = value as string;\n        out.push(\n            `def: \"${escapeOboQuoted(counted(f.stats, text))}\" ${xrefList(f, ids, \"def\")}${f.cursor.block(\"def\", text)}`,\n        );\n    },\n    xref(f, _tag, value, out) {\n        for (const id of value as string[]) {\n            out.push(`xref: ${xrefText(f, id, null)}${f.cursor.block(\"xref\", id)}`);\n        }\n    },\n    synonym(f, _tag, value, out) {\n        for (const s of value as {\n            text: string;\n            scope: string;\n            type: string | null;\n            xrefs: string[];\n            qualifiers?: unknown;\n        }[]) {\n            const type = s.type === null ? \"\" : ` ${escapeOboWord(s.type)}`;\n            out.push(\n                `synonym: \"${escapeOboQuoted(counted(f.stats, s.text))}\" ${s.scope}${type} ${xrefList(f, s.xrefs, \"synonym\")}${blockOf(s.qualifiers)}`,\n            );\n        }\n    },\n    intersection_of(_f, _tag, value, out) {\n        for (const x of value as { relation: string | null; target: string; qualifiers?: unknown }[]) {\n            const relation = x.relation === null ? \"\" : `${escapeOboWord(x.relation)} `;\n            out.push(`intersection_of: ${relation}${escapeOboWord(x.target)}${blockOf(x.qualifiers)}`);\n        }\n    },\n    property_value(f, _tag, value, out) {\n        for (const x of value as { relation: string; value: string; datatype: string | null; qualifiers?: unknown }[]) {\n            const datatype = x.datatype === null ? \"\" : ` ${escapeOboWord(x.datatype)}`;\n            const literal =\n                x.datatype === null && isOboWord(x.value)\n                    ? escapeOboWord(x.value)\n                    : `\"${escapeOboQuoted(counted(f.stats, x.value))}\"${datatype}`;\n            out.push(`property_value: ${escapeOboWord(x.relation)} ${literal}${blockOf(x.qualifiers)}`);\n        }\n    },\n    holds_over_chain: chainLines,\n    equivalent_to_chain: chainLines,\n    expand_assertion_to: expansionLines,\n    expand_expression_to: expansionLines,\n    [UNRECOGNIZED](f, _tag, value, out) {\n        for (const [unknown, values] of Object.entries(value as Record<string, string[]>)) {\n            for (const v of values) {\n                out.push(`${escapeTag(unknown)}: ${escapeOboValue(counted(f.stats, v))}`);\n            }\n        }\n    },\n};\n\n/**\n * The clauses of a relation chain tag (`holds_over_chain`, `equivalent_to_chain`).\n * @param f - the frame state\n * @param tag - the tag\n * @param value - the cell: pairs of relations\n * @param out - the lines\n */\nfunction chainLines(f: FrameState, tag: string, value: unknown, out: string[]): void {\n    for (const [a, b] of value as [string, string][]) {\n        const pair = `${a} ${b}`;\n        out.push(`${tag}: ${escapeOboWord(a)} ${escapeOboWord(b)}${f.cursor.block(tag, pair)}`);\n    }\n}\n\n/**\n * The clauses of a macro expansion tag (`expand_assertion_to`, `expand_expression_to`).\n * @param f - the frame state\n * @param tag - the tag\n * @param value - the cell: templates with their xrefs\n * @param out - the lines\n */\nfunction expansionLines(f: FrameState, tag: string, value: unknown, out: string[]): void {\n    for (const x of value as { template: string; xrefs: string[]; qualifiers?: unknown }[]) {\n        out.push(\n            `${tag}: \"${escapeOboQuoted(counted(f.stats, x.template))}\" ${xrefList(f, x.xrefs, tag)}${blockOf(x.qualifiers)}`,\n        );\n    }\n}\n\n/**\n * The lines of one node's frame.\n * @param p - the plan\n * @param row - the node\n * @param stats - the counters\n * @returns the lines, the frame header first\n */\nfunction frameLines(p: Plan, row: number, stats: FrameStats): string[] {\n    const qualifiersColumn = p.tags.get(\"obo.qualifiers\");\n    const f: FrameState = {\n        p,\n        row,\n        cursor: new QualifierCursor(qualifiersColumn === undefined ? undefined : cellOf(qualifiersColumn, row)),\n        described: new Set(),\n        stats,\n    };\n    const out = [`[${p.kinds[row]}]`, `id: ${escapeOboWord(p.ids[row])}`];\n    for (const tag of TAG_ORDER) {\n        if (tag === \"name\") {\n            nameLine(f, out);\n        } else if (tag === \"property_value\") {\n            propertyValueLines(f, out);\n        } else if (tag === EDGES) {\n            edgeLines(f, out);\n        } else {\n            const column = p.tags.get(tag);\n            if (column !== undefined) {\n                tagLines(f, tag, column, out);\n            }\n        }\n    }\n    stats.qualifiersPlaced &&= f.cursor.placed();\n    return out;\n}\n\n/**\n * The name clause of a frame, from the label column.\n * @param f - the frame state\n * @param out - the lines\n */\nfunction nameLine(f: FrameState, out: string[]): void {\n    const name = f.p.label === null ? undefined : cellOf(f.p.label, f.row);\n    if (typeof name === \"string\") {\n        out.push(`name: ${escapeOboValue(counted(f.stats, name))}${f.cursor.block(\"name\", name)}`);\n    }\n}\n\n/**\n * The property_value clauses of a frame: the original id of a rewritten one, the property_value\n * column, then the property-value columns.\n * @param f - the frame state\n * @param out - the lines\n */\nfunction propertyValueLines(f: FrameState, out: string[]): void {\n    const { p, row } = f;\n    const original = p.originals.get(row);\n    if (original !== undefined) {\n        // as JSON text, so a carriage return in the original survives\n        out.push(`property_value: ${ORIGINAL_ID} \"${escapeOboQuoted(JSON.stringify(original))}\" xsd:string`);\n    }\n    const column = p.tags.get(\"property_value\");\n    if (column !== undefined) {\n        tagLines(f, \"property_value\", column, out);\n    }\n    for (const prop of p.properties) {\n        for (const line of propertyLines(prop, row, f.stats)) {\n            out.push(`property_value: ${line}`);\n        }\n    }\n}\n\n/**\n * The edge clauses of a frame: 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