@jbrowse/jexl 4.0.1 → 5.0.0

package/dist/Lexer.js

@@ -4,15 +4,20 @@
  * Copyright 2020 Tom Shawver
  */
 Object.defineProperty(exports, "__esModule", { value: true });
+const errors_ts_1 = require("./errors.js");
 // what an identifier and a number look like, written once: the split regex
 // below carves elements out of the expression with these, and _createToken
 // then re-tests the elements it produced. Two spellings of either would
 // disagree on some input, and each disagreement is an "Invalid expression
 // token" for something the splitter was happy to produce.
 const identChars = String.raw `a-zA-Zа-яА-Я_\u00C0-\u00D6\u00D8-\u00F6\u00F8-\u00FF$`;
-const identPattern = `[${identChars}][${identChars}0-9]*`;
+const identPart = `[${identChars}0-9]`;
+const identPattern = `[${identChars}]${identPart}*`;
+// a word operator such as `in`, but not part of a longer name. \b would do only
+// for ASCII names, and split `in$` or `inà` into the operator and a remainder
+const wholeWord = (word) => `(?<!${identPart})${word}(?!${identPart})`;
 // unsigned: whether a leading '-' negates is decided separately, in getTokens
-const numberPattern = String.raw `(?:(?:[0-9]*\.[0-9]+)|[0-9]+)`;
+const numberPattern = String.raw `(?:(?:[0-9]*\.[0-9]+)|[0-9]+)(?:[eE][+-]?[0-9]+)?`;
 const numericRegex = new RegExp(`^-?${numberPattern}$`);
 const identRegex = new RegExp(`^${identPattern}$`);
 const escEscRegex = /\\\\/g;
@@ -32,11 +37,10 @@ const preOpRegexElems = [
     String.raw `"(?:(?:\\")|[^"])*"`,
     // Whitespace
     String.raw `\s+`,
-    // Booleans
-    String.raw `\btrue\b`,
-    String.raw `\bfalse\b`
+    // ahead of the grammar's '.', so that '.5' is a number rather than a dot
+    numberPattern
 ];
-const postOpRegexElems = [identPattern, numberPattern];
+const postOpRegexElems = [identPattern];
 const unaryMinusToken = () => ({
     type: 'unaryOp',
     value: '-',
@@ -50,7 +54,8 @@ const minusNegatesAfter = new Set([
     'question',
     'colon',
     'comma',
-    'semicolon'
+    'semicolon',
+    'arrow'
 ]);
 /**
  * Lexer handles the lexical parsing of a Jexl string. Its responsibility is to
@@ -105,6 +110,7 @@ class Lexer {
         // 1") accumulates on the minus rather than on the token before it, which
         // is what lets the parser's error messages quote the expression verbatim.
         let pendingMinus;
+        let offset = 0;
         for (const element of elements) {
             if (this._isWhitespace(element)) {
                 const last = pendingMinus ?? tokens.at(-1);
@@ -123,20 +129,21 @@ class Lexer {
             else if (pendingMinus) {
                 if (numericRegex.exec(element)) {
                     // fold the sign into the number, so "-1" stays a single literal
-                    const token = this._createToken('-' + element);
+                    const token = this._createToken('-' + element, offset);
                     token.raw = pendingMinus.raw + element;
                     tokens.push(token);
                 }
                 else {
                     // anything else gets a standalone prefix operator, letting "-x",
                     // "-(a + b)" and "-foo.bar" negate a computed value
-                    tokens.push(pendingMinus, this._createToken(element));
+                    tokens.push(pendingMinus, this._createToken(element, offset));
                 }
                 pendingMinus = undefined;
             }
             else {
-                tokens.push(this._createToken(element));
+                tokens.push(this._createToken(element, offset));
             }
+            offset += element.length;
         }
         // Catch a - at the end of the string. Let the parser handle that issue.
         if (pendingMinus) {
@@ -185,7 +192,7 @@ class Lexer {
      * @throws {Error} if the provided string is not a valid expression element.
      * @private
      */
-    _createToken(element) {
+    _createToken(element, offset = 0) {
         const token = {
             type: 'literal',
             value: element,
@@ -193,7 +200,7 @@ class Lexer {
         };
         if (element.startsWith('`')) {
             token.type = 'templateString';
-            token.value = this._parseTemplateString(element);
+            token.value = this._parseTemplateString(element, offset);
             return token;
         }
         else if (element.startsWith('"') || element.startsWith("'")) {
@@ -205,6 +212,9 @@ class Lexer {
         else if (element === 'true' || element === 'false') {
             token.value = element === 'true';
         }
+        else if (element === 'null') {
+            token.value = null;
+        }
         else if (Object.hasOwn(this._grammar.elements, element)) {
             token.type = this._grammar.elements[element].type;
         }
@@ -212,24 +222,22 @@ class Lexer {
             token.type = 'identifier';
         }
         else {
-            throw new Error(`Invalid expression token: ${element}`);
+            throw new errors_ts_1.JexlSyntaxError(`Invalid expression token: ${element}`, offset);
         }
         return token;
     }
     /**
      * Escapes a string so that it can be treated as a string literal within a
-     * regular expression.
+     * regular expression. A word such as `in` also stops matching inside a
+     * longer name.
      * @param {string} str The string to be escaped
      * @returns {string} the RegExp-escaped string.
      * @see https://developer.mozilla.org/en/docs/Web/JavaScript/Guide/Regular_Expressions
      * @private
      */
     _escapeRegExp(str) {
-        str = str.replaceAll(/[.*+?^${}()|[\]\\]/g, String.raw `\$&`);
-        if (identRegex.exec(str)) {
-            str = String.raw `\b` + str + String.raw `\b`;
-        }
-        return str;
+        const escaped = str.replaceAll(/[.*+?^${}()|[\]\\]/g, String.raw `\$&`);
+        return identRegex.exec(str) ? wholeWord(escaped) : escaped;
     }
     /**
      * Gets a RegEx object appropriate for splitting a Jexl string into its core
@@ -299,7 +307,7 @@ class Lexer {
             .replaceAll(escQuoteRegex[quote], quote)
             .replaceAll(escEscRegex, '\\');
     }
-    _parseTemplateString(str) {
+    _parseTemplateString(str, offset = 0) {
         const parts = [];
         let current = 1;
         let staticStart = 1;
@@ -343,7 +351,7 @@ class Lexer {
                     current++;
                 }
                 if (braceDepth !== 0) {
-                    throw new Error(`Unclosed interpolation in template string: ${str}`);
+                    throw new errors_ts_1.JexlSyntaxError(`Unclosed interpolation in template string: ${str}`, offset + interpStart - '${'.length);
                 }
                 parts.push({
                     type: 'interpolation',

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package/dist/analyze.d.ts

@@ -0,0 +1,84 @@
+import type { AstNode } from './types.ts';
+export type PathKey = string | number;
+/**
+ * A value the expression reads out of its context: the variable `root`, then
+ * each literal key in `path`. `dynamic` means a computed key followed, so the
+ * read reaches somewhere under `path` that only evaluation can name.
+ *
+ * A dot and a bracket both add a key.
+ */
+export interface Read {
+    root: string;
+    path: PathKey[];
+    dynamic?: true;
+}
+export type CallArg = {
+    type: 'literal';
+    value: string | number | boolean | null;
+} | {
+    type: 'path';
+    read: Read;
+} | {
+    type: 'dynamic';
+};
+/** A path under the row, the record a per-row expression is evaluated for. */
+export interface Field {
+    path: PathKey[];
+    dynamic?: true;
+}
+export interface Call {
+    name: string;
+    args: CallArg[];
+}
+export interface Analysis {
+    /** The context variables read, in the order first read. */
+    variables: string[];
+    /**
+     * Every path whose value the expression uses, in the order first used. A
+     * path only extended, as `feature` is in `feature.score`, is not a use.
+     */
+    reads: Read[];
+    /** The reads that are fields of the row, as `row` and `env` say. */
+    fields: Field[];
+    /** The paths whose value the expression returns as is. */
+    returns: Read[];
+    /**
+     * Whether the expression is only a path: a name, then dots and literal
+     * subscripts, as in `score` or `feature.INFO.DP[0]`. Its one read is then
+     * its value, which a host can read without jexl.
+     */
+    bare: boolean;
+    /** Every call, outermost first, including accessor calls. */
+    calls: Call[];
+    /** The names the expression writes into its context. */
+    assigned: string[];
+}
+export interface AnalyzeOptions {
+    /**
+     * Functions that read a path: `name(subject, ...keys)` reads the subject,
+     * then this prefix, then each key. `{ get: [] }` makes `get(feature, 'x')`
+     * and `feature.get('x')` both read `feature.x`.
+     */
+    accessors?: Record<string, readonly PathKey[]>;
+    /** The variable holding the row, whose reads `fields` lists: `'feature'`. */
+    row?: string;
+    /**
+     * For a host that binds each of the row's fields as a variable, so that
+     * `pvalue` means the row's `pvalue`: the variables it binds to anything
+     * else. Every other variable the expression reads is then a field.
+     */
+    env?: readonly string[];
+}
+/**
+ * Lists what an expression reads from its context, without evaluating it or
+ * consulting any registered function.
+ *
+ * A name assigned earlier in the expression is a local: `x = feature.score;
+ * x > 1` reads `feature.score` and no `x`. An assignment that may not run — in
+ * a conditional's branch, or right of a binary operator, which may short-circuit
+ * — counts its value as read and binds nothing past that operand, so a later
+ * read of the name is a context read.
+ *
+ * Every path evaluation reads is reported, or a prefix of it is.
+ */
+export declare function analyze(ast: AstNode | null, { accessors, row, env }?: AnalyzeOptions): Analysis;

package/dist/analyze.js

@@ -0,0 +1,259 @@
+"use strict";
+/*
+ * Jexl
+ * Copyright 2020 Tom Shawver
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.analyze = analyze;
+function literalKey(node) {
+    const value = literalValue(node);
+    return typeof value === 'boolean' ? String(value) : (value ?? undefined);
+}
+function literalValue(ast) {
+    const node = ast;
+    if (node.type === 'Literal') {
+        return node.value;
+    }
+    if (node.type === 'TemplateLiteral' &&
+        node.parts.every((part) => part.type === 'static')) {
+        return node.parts.map((part) => part.value).join('');
+    }
+    return undefined;
+}
+function extend(read, keys, dynamic = false) {
+    if (read.dynamic) {
+        return read;
+    }
+    const path = [...read.path, ...keys];
+    return dynamic
+        ? { root: read.root, path, dynamic }
+        : { root: read.root, path };
+}
+function isBarePath(ast) {
+    const node = ast;
+    if (node.type === 'Identifier') {
+        return !node.from || isBarePath(node.from);
+    }
+    return (node.type === 'FilterExpression' &&
+        literalKey(node.expr) !== undefined &&
+        isBarePath(node.subject));
+}
+function fieldOf({ root, path, dynamic }, row, env) {
+    const fieldPath = root === row
+        ? path
+        : env && !env.includes(root)
+            ? [root, ...path]
+            : undefined;
+    return (fieldPath && (dynamic ? { path: fieldPath, dynamic } : { path: fieldPath }));
+}
+function classify(node, value) {
+    const literal = literalValue(node);
+    if (literal !== undefined) {
+        return { type: 'literal', value: literal };
+    }
+    return value.length === 1
+        ? { type: 'path', read: value[0] }
+        : { type: 'dynamic' };
+}
+/**
+ * Lists what an expression reads from its context, without evaluating it or
+ * consulting any registered function.
+ *
+ * A name assigned earlier in the expression is a local: `x = feature.score;
+ * x > 1` reads `feature.score` and no `x`. An assignment that may not run — in
+ * a conditional's branch, or right of a binary operator, which may short-circuit
+ * — counts its value as read and binds nothing past that operand, so a later
+ * read of the name is a context read.
+ *
+ * Every path evaluation reads is reported, or a prefix of it is.
+ */
+function analyze(ast, { accessors = {}, row, env } = {}) {
+    const reads = new Map();
+    const calls = [];
+    const assigned = new Set();
+    function consume(value) {
+        for (const read of value) {
+            const key = JSON.stringify([read.root, read.path, read.dynamic]);
+            if (!reads.has(key)) {
+                reads.set(key, read);
+            }
+        }
+    }
+    function use(node, scope) {
+        consume(walk(node, scope));
+    }
+    function release(scope, outer) {
+        for (const [name, binding] of scope) {
+            if (!binding.used && outer?.get(name) !== binding) {
+                consume(binding.value);
+            }
+        }
+    }
+    function branch(node, scope) {
+        if (!node) {
+            return [];
+        }
+        const inner = new Map(scope);
+        const value = walk(node, inner);
+        release(inner, scope);
+        return value;
+    }
+    function call(node, scope) {
+        const record = { name: node.name, args: [] };
+        calls.push(record);
+        const [subjectNode, ...keyNodes] = node.args;
+        const prefix = Object.hasOwn(accessors, node.name)
+            ? accessors[node.name]
+            : undefined;
+        if (!prefix || !subjectNode) {
+            for (const arg of node.args) {
+                const value = walk(arg, scope);
+                record.args.push(classify(arg, value));
+                consume(value);
+            }
+            return [];
+        }
+        const subject = walk(subjectNode, scope);
+        record.args.push(classify(subjectNode, subject));
+        const keys = [...prefix];
+        let dynamic = false;
+        for (const arg of keyNodes) {
+            const key = literalKey(arg);
+            if (key === undefined) {
+                const value = walk(arg, scope);
+                record.args.push(classify(arg, value));
+                consume(value);
+                dynamic = true;
+            }
+            else {
+                record.args.push({ type: 'literal', value: literalValue(arg) });
+                if (!dynamic) {
+                    keys.push(key);
+                }
+            }
+        }
+        return subject.map((read) => extend(read, keys, dynamic));
+    }
+    function walk(ast, scope) {
+        const node = ast;
+        switch (node.type) {
+            case 'Literal': {
+                return [];
+            }
+            case 'Identifier': {
+                if (node.from) {
+                    return walk(node.from, scope).map((read) => extend(read, [node.value]));
+                }
+                const binding = scope.get(node.value);
+                if (binding) {
+                    binding.used = true;
+                    return binding.value;
+                }
+                return [{ root: node.value, path: [] }];
+            }
+            case 'FilterExpression': {
+                const subject = walk(node.subject, scope);
+                const key = literalKey(node.expr);
+                if (key !== undefined) {
+                    return subject.map((read) => extend(read, [key]));
+                }
+                use(node.expr, scope);
+                return subject.map((read) => extend(read, [], true));
+            }
+            case 'FunctionCall': {
+                return call(node, scope);
+            }
+            case 'ConditionalExpression': {
+                const test = walk(node.test, scope);
+                consume(test);
+                const consequent = node.consequent
+                    ? branch(node.consequent, scope)
+                    : test;
+                return [...consequent, ...branch(node.alternate, scope)];
+            }
+            case 'BinaryExpression': {
+                use(node.left, scope);
+                consume(branch(node.right, scope));
+                return [];
+            }
+            case 'UnaryExpression': {
+                use(node.right, scope);
+                return [];
+            }
+            case 'ArrayLiteral': {
+                for (const item of node.value) {
+                    use(item, scope);
+                }
+                return [];
+            }
+            case 'ObjectLiteral': {
+                for (const value of Object.values(node.value)) {
+                    use(value, scope);
+                }
+                return [];
+            }
+            case 'TemplateLiteral': {
+                for (const part of node.parts) {
+                    if (part.type === 'expression') {
+                        use(part.value, scope);
+                    }
+                }
+                return [];
+            }
+            case 'SequenceExpression': {
+                const exprs = node.expressions;
+                for (const expr of exprs.slice(0, -1)) {
+                    const value = walk(expr, scope);
+                    if (expr.type !== 'AssignmentExpression') {
+                        consume(value);
+                    }
+                }
+                return walk(exprs.at(-1), scope);
+            }
+            case 'AssignmentExpression': {
+                const value = walk(node.right, scope);
+                const name = node.left.value;
+                const previous = scope.get(name);
+                if (previous && !previous.used) {
+                    consume(previous.value);
+                }
+                scope.set(name, { value, used: false });
+                assigned.add(name);
+                return value;
+            }
+            case 'Lambda': {
+                const inner = new Map(scope);
+                for (const param of node.params) {
+                    inner.set(param, { value: [], used: true });
+                }
+                use(node.body, inner);
+                return [];
+            }
+            default: {
+                throw new Error(`Corrupt AST: unknown node type '${ast.type}'`);
+            }
+        }
+    }
+    const scope = new Map();
+    const returns = ast ? walk(ast, scope) : [];
+    consume(returns);
+    release(scope);
+    const readList = [...reads.values()];
+    const fields = new Map();
+    for (const read of readList) {
+        const field = fieldOf(read, row, env);
+        if (field) {
+            fields.set(JSON.stringify(field), field);
+        }
+    }
+    return {
+        variables: [...new Set(readList.map((read) => read.root))],
+        reads: readList,
+        fields: [...fields.values()],
+        returns,
+        bare: ast !== null && isBarePath(ast),
+        calls,
+        assigned: [...assigned]
+    };
+}
+//# sourceMappingURL=analyze.js.map

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package/dist/check.d.ts

@@ -0,0 +1,109 @@
+import type { AnalyzeOptions } from './analyze.ts';
+import type { AstNode } from './types.ts';
+/**
+ * How many values a field holds: one, a list of exactly that many when a
+ * number, or a list whose length follows the record, as VCF's `Number=A`, `R`,
+ * `G` and `.` do.
+ */
+export type Cardinality = 'one' | 'perAlt' | 'perAllele' | 'perGenotype' | 'many' | number;
+/**
+ * One field of a row, as a file header declares it. A `record` field's own
+ * fields are further entries whose path extends its path, including when the
+ * record is a list of them. A path key of `*` stands for every key of a map,
+ * such as a VCF record's sample names. An entry with an empty path describes
+ * the row itself.
+ */
+export interface FieldSchema {
+    path: readonly string[];
+    type: 'number' | 'string' | 'boolean' | 'flag' | 'record';
+    cardinality?: Cardinality;
+    integer?: boolean;
+    description?: string;
+    /** Every value the field takes, where the header enumerates them. */
+    categories?: readonly string[];
+    domain?: readonly [number, number];
+    /** For a record: its fields were observed in data rather than declared. */
+    open?: boolean;
+}
+interface FromField {
+    field?: FieldSchema;
+}
+export type Type = {
+    kind: 'unknown';
+} | {
+    kind: 'undefined';
+} | (FromField & {
+    kind: 'number';
+    values?: readonly number[];
+    domain?: readonly [number, number];
+}) | (FromField & {
+    kind: 'string';
+    values?: readonly string[];
+}) | (FromField & {
+    kind: 'boolean';
+}) | (FromField & {
+    kind: 'list';
+    of: Type;
+    cardinality: Exclude<Cardinality, 'one'>;
+}) | (FromField & {
+    kind: 'record';
+    fields: ReadonlyMap<string, Type>;
+    each?: Type;
+    open: boolean;
+}) | {
+    kind: 'union';
+    of: readonly Type[];
+} | {
+    kind: 'lambda';
+    returns: Type;
+};
+export type ParamType = 'number' | 'string' | 'boolean' | 'list' | 'record' | 'any' | 'member' | 'lambda';
+export interface Signature {
+    params: readonly (ParamType | readonly ParamType[])[];
+    /** How many trailing params a call may leave out. */
+    optional?: number;
+    /** Whether the last param repeats. */
+    variadic?: boolean;
+    returns?: 'number' | 'string' | 'boolean' | Type | ((args: readonly Type[]) => Type);
+}
+export type Severity = 'error' | 'warning' | 'info';
+export type DiagnosticCode = 'unknown-variable' | 'unknown-field' | 'unknown-function' | 'arity' | 'argument-type' | 'list-operand' | 'list-lengths' | 'invalid-pattern' | 'string-numeric' | 'never-equal' | 'unknown-category' | 'index-scalar' | 'index-range' | 'dot-through-list' | 'dotted-key';
+export interface Diagnostic {
+    code: DiagnosticCode;
+    severity: Severity;
+    message: string;
+    node: AstNode;
+    /** Replacements for `node`'s text, best first. */
+    suggestions?: string[];
+}
+export interface CheckOptions {
+    schema?: readonly FieldSchema[];
+    functions?: Readonly<Record<string, Signature>>;
+    accessors?: AnalyzeOptions['accessors'];
+    /** The variable holding the row. Without one, every free name is a field. */
+    row?: string;
+    /**
+     * The other variables the host binds, and their types. When given, any name
+     * that is neither these, the row nor a field is reported.
+     */
+    env?: Readonly<Record<string, Type>>;
+}
+export interface CheckResult {
+    diagnostics: Diagnostic[];
+    type: Type;
+}
+export declare const UNKNOWN: Type;
+/**
+ * Renders a tree back to expression text, for messages and suggestions. The
+ * text parses back to the same tree.
+ */
+export declare function print(ast: AstNode): string;
+/** The type of a row whose fields `schema` declares. */
+export declare function recordOf(schema: readonly FieldSchema[]): Type;
+export declare function union(a: Type, b: Type): Type;
+/**
+ * Checks an expression against the fields a host's data declares and the
+ * functions it registers, without evaluating it, and infers what it answers.
+ */
+export declare function check(ast: AstNode | null, { schema, functions, accessors, row, env }?: CheckOptions): CheckResult;
+export {};