@de-otio/bibcheck 0.1.0

package/dist/output/sarif.js

@@ -0,0 +1,322 @@
+/**
+ * SARIF v2.1.0 renderer for bibcheck output.
+ *
+ * Uses node-sarif-builder for the structural boilerplate (tool/driver, rules,
+ * results) and then post-processes the resulting object to add:
+ *   - originalUriBaseIds so that relative artifact URIs resolve correctly
+ *   - partialFingerprints (sha256-based, stable across runs) for deduplication
+ *
+ * The library does not expose a first-class API for those two fields, so they
+ * are injected directly onto the mutable run/result objects that the builders
+ * expose as public properties (`.run` and `.result`). This is the documented
+ * escape hatch in node-sarif-builder.
+ *
+ * Worklist items are NOT emitted as SARIF results. They are informational and
+ * would cause spurious CI failures if surfaced as findings.
+ */
+import { createHash } from 'node:crypto';
+import { SarifBuilder, SarifRunBuilder, SarifResultBuilder, SarifRuleBuilder, } from 'node-sarif-builder';
+// ---------------------------------------------------------------------------
+// Constants
+// ---------------------------------------------------------------------------
+const INFORMATION_URI = 'https://github.com/de-otio/bibcheck';
+const DOCS_BASE = 'https://github.com/de-otio/bibcheck/blob/main/docs/output-schema.md';
+const STATIC_RULES = [
+    {
+        id: 'bibcheck/existence/metadata-mismatch',
+        shortDescription: 'Existence check found a metadata mismatch against the databases.',
+        anchor: 'existence-metadata-mismatch',
+    },
+    {
+        id: 'bibcheck/existence/not-found-in-databases',
+        shortDescription: 'The entry was not found in any applicable bibliographic database (a fabrication signal).',
+        anchor: 'existence-not-found-in-databases',
+    },
+    {
+        id: 'bibcheck/existence/unverifiable',
+        shortDescription: 'Existence of the entry could not be verified in any database.',
+        anchor: 'existence-unverifiable',
+    },
+    {
+        id: 'bibcheck/identifiers/malformed',
+        shortDescription: 'A DOI/ISBN/URL identifier is malformed or has a bad checksum (a fabrication signal).',
+        anchor: 'identifiers-malformed',
+    },
+    {
+        id: 'bibcheck/canonical/dead-url',
+        shortDescription: 'The canonical URL for this entry is dead (no response).',
+        anchor: 'canonical-dead-url',
+    },
+    {
+        id: 'bibcheck/canonical/wrong-host',
+        shortDescription: 'The canonical URL points to a non-approved host.',
+        anchor: 'canonical-wrong-host',
+    },
+    {
+        id: 'bibcheck/canonical/live-url-not-archived-snapshot',
+        shortDescription: 'The URL is live but is not a stable archived snapshot.',
+        anchor: 'canonical-live-url-not-archived-snapshot',
+    },
+    {
+        id: 'bibcheck/canonical/no-url-on-pre-doi-entry',
+        shortDescription: 'A pre-DOI entry is missing a canonical URL.',
+        anchor: 'canonical-no-url-on-pre-doi-entry',
+    },
+    {
+        id: 'bibcheck/linkage/unresolved',
+        shortDescription: 'A @citekey reference in the prose has no matching bibliography entry.',
+        anchor: 'linkage-unresolved',
+    },
+    {
+        id: 'bibcheck/linkage/orphan',
+        shortDescription: 'A bibliography entry is never cited in any document (informational; reverse linkage).',
+        anchor: 'linkage-orphan',
+    },
+];
+// ---------------------------------------------------------------------------
+// Fingerprint helper
+// ---------------------------------------------------------------------------
+function fingerprint(ruleId, fileUri, startLine, messageText) {
+    const payload = JSON.stringify({ ruleId, fileUri, startLine, messageText });
+    return createHash('sha256').update(payload).digest('hex').slice(0, 16);
+}
+// ---------------------------------------------------------------------------
+// Result builders
+// ---------------------------------------------------------------------------
+/** Add a result to the run with a partialFingerprint attached. */
+function addResult(sarifRunBuilder, opts) {
+    const builder = new SarifResultBuilder();
+    const initOpts = {
+        level: opts.level,
+        messageText: opts.messageText,
+        ruleId: opts.ruleId,
+        fileUri: opts.fileUri,
+    };
+    // startLine must be >= 1 for the library; 0 means "no line info"
+    if (opts.startLine != null && opts.startLine >= 1) {
+        initOpts.startLine = opts.startLine;
+    }
+    builder.initSimple(initOpts);
+    // Inject uriBaseId so the relative URI resolves against PROJECTROOT.
+    const physLoc = builder.result.locations?.[0]?.physicalLocation;
+    if (physLoc?.artifactLocation) {
+        physLoc.artifactLocation.uriBaseId = 'PROJECTROOT';
+    }
+    // Inject partialFingerprints for deduplication.
+    const fp = fingerprint(opts.ruleId, opts.fileUri, opts.startLine ?? 0, opts.messageText);
+    builder.result['partialFingerprints'] = {
+        bibcheckV1: fp,
+    };
+    sarifRunBuilder.addResult(builder);
+}
+// ---------------------------------------------------------------------------
+// Existence findings
+// ---------------------------------------------------------------------------
+function addExistenceResults(output, sarifRunBuilder) {
+    for (const entry of output.entries) {
+        const existence = entry.existence;
+        if (existence == null)
+            continue;
+        if (existence.status === 'metadata-mismatch') {
+            addResult(sarifRunBuilder, {
+                ruleId: 'bibcheck/existence/metadata-mismatch',
+                level: 'error',
+                messageText: `Existence metadata mismatch for @${entry.citekey}: database records do not match the bibliography entry.`,
+                fileUri: 'sources.json',
+            });
+        }
+        else if (existence.status === 'not-found-in-databases') {
+            // Absence is a fabrication signal and gates by default (Q1).
+            addResult(sarifRunBuilder, {
+                ruleId: 'bibcheck/existence/not-found-in-databases',
+                level: 'error',
+                messageText: `@${entry.citekey} was not found in any applicable bibliographic database.`,
+                fileUri: 'sources.json',
+            });
+        }
+    }
+}
+// ---------------------------------------------------------------------------
+// Identifier findings (T21/T22): malformed/bad-checksum local identifiers
+// ---------------------------------------------------------------------------
+function addIdentifierResults(output, sarifRunBuilder) {
+    for (const entry of output.entries) {
+        const ids = entry.identifiers;
+        if (ids == null)
+            continue;
+        const problems = [];
+        if (ids.doi === 'malformed')
+            problems.push('DOI malformed');
+        if (ids.isbn === 'malformed')
+            problems.push('ISBN malformed');
+        if (ids.isbn === 'bad-checksum')
+            problems.push('ISBN bad checksum');
+        if (ids.url === 'malformed')
+            problems.push('URL malformed');
+        if (problems.length === 0)
+            continue;
+        addResult(sarifRunBuilder, {
+            ruleId: 'bibcheck/identifiers/malformed',
+            level: 'error',
+            messageText: `Malformed identifier for @${entry.citekey}: ${problems.join(', ')}.`,
+            fileUri: 'sources.json',
+        });
+    }
+}
+// ---------------------------------------------------------------------------
+// Canonical findings
+// ---------------------------------------------------------------------------
+const CANONICAL_ERROR_STATUSES = new Set([
+    'dead-url',
+    'wrong-host',
+    'live-url-not-archived-snapshot',
+    'no-url-on-pre-doi-entry',
+]);
+function addCanonicalResults(output, sarifRunBuilder) {
+    for (const entry of output.entries) {
+        const canonical = entry.canonical;
+        if (canonical == null)
+            continue;
+        if (!CANONICAL_ERROR_STATUSES.has(canonical.status))
+            continue;
+        const urlPart = canonical.url != null ? ` (${canonical.url})` : '';
+        addResult(sarifRunBuilder, {
+            ruleId: `bibcheck/canonical/${canonical.status}`,
+            level: 'error',
+            messageText: `Canonical URL issue [${canonical.status}] for @${entry.citekey}${urlPart}.`,
+            fileUri: 'sources.json',
+        });
+    }
+}
+// ---------------------------------------------------------------------------
+// Linkage findings
+// ---------------------------------------------------------------------------
+function addLinkageResults(output, sarifRunBuilder) {
+    for (const entry of output.linkage) {
+        if (entry.status !== 'unresolved')
+            continue;
+        const sortedRefs = [...entry.references].sort((a, b) => {
+            const fc = a.file.localeCompare(b.file);
+            return fc !== 0 ? fc : a.line - b.line;
+        });
+        for (const ref of sortedRefs) {
+            addResult(sarifRunBuilder, {
+                ruleId: 'bibcheck/linkage/unresolved',
+                level: 'error',
+                messageText: `Unresolved @${entry.citekey} reference — no matching bibliography entry.`,
+                fileUri: ref.file,
+                startLine: ref.line,
+            });
+        }
+    }
+}
+/**
+ * Orphaned bibliography entries (reverse linkage, H2). Emitted at `note` level
+ * so they surface in Code Scanning as informational annotations and never
+ * cause a CI failure. Bibliography-level, so anchored to sources.json.
+ */
+function addOrphanResults(output, sarifRunBuilder) {
+    for (const entry of output.linkage) {
+        if (entry.status !== 'orphan')
+            continue;
+        addResult(sarifRunBuilder, {
+            ruleId: 'bibcheck/linkage/orphan',
+            level: 'note',
+            messageText: `@${entry.citekey} is in the bibliography but is never cited in any document (informational).`,
+            fileUri: 'sources.json',
+        });
+    }
+}
+// ---------------------------------------------------------------------------
+// Phrase flag findings
+// ---------------------------------------------------------------------------
+function addPhraseFlagResults(output, sarifRunBuilder) {
+    for (const flag of output.phraseFlags) {
+        if (flag.status !== 'flagged')
+            continue;
+        addResult(sarifRunBuilder, {
+            ruleId: `bibcheck/phrase/${flag.patternKey}`,
+            level: 'warning',
+            messageText: `phrase: "${flag.matchedText}"`,
+            fileUri: flag.file,
+            startLine: flag.line,
+        });
+    }
+}
+// ---------------------------------------------------------------------------
+// Dynamic rule collection (phrase pattern rules)
+// ---------------------------------------------------------------------------
+function collectPhraseRules(output) {
+    const seen = new Set();
+    const rules = [];
+    for (const flag of output.phraseFlags) {
+        const id = `bibcheck/phrase/${flag.patternKey}`;
+        if (!seen.has(id)) {
+            seen.add(id);
+            rules.push({
+                id,
+                shortDescription: `Phrase denylist match for pattern key "${flag.patternKey}".`,
+                anchor: `phrase-${flag.patternKey}`,
+            });
+        }
+    }
+    return rules;
+}
+// ---------------------------------------------------------------------------
+// Public API
+// ---------------------------------------------------------------------------
+/**
+ * Render a validated Output as a SARIF v2.1.0 JSON string.
+ *
+ * The SARIF document contains one run with:
+ * - tool.driver with all applicable rules defined
+ * - originalUriBaseIds.PROJECTROOT so relative file URIs resolve correctly
+ * - one result per finding (existence mismatches, canonical errors, linkage
+ *   unresolved, phrase flags), with partialFingerprints for deduplication
+ *
+ * Worklist items are not emitted as SARIF results (they are informational).
+ * Acknowledged phrase flags are not emitted (only status: 'flagged' entries).
+ */
+export function renderSarif(output) {
+    // Collect dynamic rules from phrase flags.
+    const phraseRules = collectPhraseRules(output);
+    const allRuleDefs = [...STATIC_RULES, ...phraseRules];
+    // Build the run.
+    const version = output.tool.version;
+    const sarifRunBuilder = new SarifRunBuilder().initSimple({
+        toolDriverName: 'bibcheck',
+        toolDriverVersion: version,
+        url: INFORMATION_URI,
+    });
+    // Add semanticVersion directly (node-sarif-builder doesn't expose a setter).
+    sarifRunBuilder.run.tool.driver['semanticVersion'] =
+        version;
+    // Register all rules.
+    for (const ruleDef of allRuleDefs) {
+        const ruleBuilder = new SarifRuleBuilder().initSimple({
+            ruleId: ruleDef.id,
+            shortDescriptionText: ruleDef.shortDescription,
+            helpUri: `${DOCS_BASE}#${ruleDef.anchor}`,
+        });
+        sarifRunBuilder.addRule(ruleBuilder);
+    }
+    // Add findings.
+    addIdentifierResults(output, sarifRunBuilder);
+    addExistenceResults(output, sarifRunBuilder);
+    addCanonicalResults(output, sarifRunBuilder);
+    addLinkageResults(output, sarifRunBuilder);
+    addOrphanResults(output, sarifRunBuilder);
+    addPhraseFlagResults(output, sarifRunBuilder);
+    // Inject originalUriBaseIds so relative URIs resolve to the project root.
+    sarifRunBuilder.run['originalUriBaseIds'] = {
+        PROJECTROOT: { uri: 'file:///$PROJECT_ROOT/' },
+    };
+    // Build the top-level SARIF document.
+    const sarifBuilder = new SarifBuilder();
+    sarifBuilder.addRun(sarifRunBuilder);
+    const sarifObj = sarifBuilder.buildSarifOutput();
+    // Override $schema to use https (the library defaults to http).
+    sarifObj['$schema'] = 'https://json.schemastore.org/sarif-2.1.0.json';
+    return JSON.stringify(sarifObj, null, 2) + '\n';
+}
+//# sourceMappingURL=sarif.js.map

package/dist/output/sarif.js.map

@@ -0,0 +1 @@
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package/dist/output/text.d.ts

@@ -0,0 +1,27 @@
+/**
+ * Compact text renderer for bibcheck output.
+ *
+ * Produces one line per finding in the format:
+ *   <file>:<line>: <level>: <message>
+ *
+ * For findings without a specific file/line (existence-layer results tied to
+ * the bibliography source, not a prose file), uses "sources.json:0" as a
+ * stand-in artifact location.
+ *
+ * A summary line is appended at the end:
+ *   <n> errors, <m> warnings, <k> notes
+ */
+import type { Output } from '../schema/output.js';
+/**
+ * Render a validated Output as a compact text string.
+ *
+ * Format: one line per finding as `<file>:<line>: <level>: <message>`,
+ * followed by a summary line with counts.
+ *
+ * Level mapping (same as SARIF):
+ * - error: existence metadata-mismatch, canonical dead-url/wrong-host/etc, linkage unresolved
+ * - warning: phrase flags (flagged, not acknowledged)
+ * - note: existence unverifiable, worklist items, orphaned bibliography entries
+ */
+export declare function renderText(output: Output): string;
+//# sourceMappingURL=text.d.ts.map

package/dist/output/text.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"text.d.ts","sourceRoot":"","sources":["../../src/output/text.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,qBAAqB,CAAC;AAyKlD;;;;;;;;;;GAUG;AACH,wBAAgB,UAAU,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CA4BjD"}

package/dist/output/text.js

@@ -0,0 +1,212 @@
+/**
+ * Compact text renderer for bibcheck output.
+ *
+ * Produces one line per finding in the format:
+ *   <file>:<line>: <level>: <message>
+ *
+ * For findings without a specific file/line (existence-layer results tied to
+ * the bibliography source, not a prose file), uses "sources.json:0" as a
+ * stand-in artifact location.
+ *
+ * A summary line is appended at the end:
+ *   <n> errors, <m> warnings, <k> notes
+ */
+// ---------------------------------------------------------------------------
+// Helpers
+// ---------------------------------------------------------------------------
+function fmt(f) {
+    return `${f.file}:${f.line}: ${f.level}: ${f.message}`;
+}
+// ---------------------------------------------------------------------------
+// Finding collectors
+// ---------------------------------------------------------------------------
+function collectExistenceFindings(output) {
+    const findings = [];
+    for (const entry of output.entries) {
+        if (entry.existence?.status === 'metadata-mismatch') {
+            findings.push({
+                file: 'sources.json',
+                line: 0,
+                level: 'error',
+                message: `existence metadata-mismatch for @${entry.citekey}`,
+            });
+        }
+        else if (entry.existence?.status === 'not-found-in-databases') {
+            // Absence is a fabrication signal and gates by default (Q1).
+            findings.push({
+                file: 'sources.json',
+                line: 0,
+                level: 'error',
+                message: `existence not-found-in-databases for @${entry.citekey}`,
+            });
+        }
+        else if (entry.existence?.status === 'unverifiable') {
+            findings.push({
+                file: 'sources.json',
+                line: 0,
+                level: 'note',
+                message: `existence unverifiable for @${entry.citekey}`,
+            });
+        }
+    }
+    return findings;
+}
+/** Malformed/bad-checksum local identifiers (T21/T22). Gating → error level. */
+function collectIdentifierFindings(output) {
+    const findings = [];
+    for (const entry of output.entries) {
+        const ids = entry.identifiers;
+        if (ids === null || ids === undefined)
+            continue;
+        const problems = [];
+        if (ids.doi === 'malformed')
+            problems.push('doi malformed');
+        if (ids.isbn === 'malformed')
+            problems.push('isbn malformed');
+        if (ids.isbn === 'bad-checksum')
+            problems.push('isbn bad-checksum');
+        if (ids.url === 'malformed')
+            problems.push('url malformed');
+        if (problems.length === 0)
+            continue;
+        findings.push({
+            file: 'sources.json',
+            line: 0,
+            level: 'error',
+            message: `identifier ${problems.join(', ')} for @${entry.citekey}`,
+        });
+    }
+    return findings;
+}
+function collectCanonicalFindings(output) {
+    const findings = [];
+    const errorStatuses = new Set([
+        'dead-url',
+        'wrong-host',
+        'live-url-not-archived-snapshot',
+        'no-url-on-pre-doi-entry',
+    ]);
+    for (const entry of output.entries) {
+        const canon = entry.canonical;
+        if (canon == null)
+            continue;
+        if (errorStatuses.has(canon.status)) {
+            const urlPart = canon.url != null ? ` (${canon.url})` : '';
+            findings.push({
+                file: 'sources.json',
+                line: 0,
+                level: 'error',
+                message: `canonical ${canon.status} for @${entry.citekey}${urlPart}`,
+            });
+        }
+    }
+    return findings;
+}
+function collectLinkageFindings(output) {
+    const findings = [];
+    for (const entry of output.linkage) {
+        if (entry.status !== 'unresolved')
+            continue;
+        const sortedRefs = [...entry.references].sort((a, b) => {
+            const fc = a.file.localeCompare(b.file);
+            return fc !== 0 ? fc : a.line - b.line;
+        });
+        for (const ref of sortedRefs) {
+            findings.push({
+                file: ref.file,
+                line: ref.line,
+                level: 'error',
+                message: `unresolved linkage @${entry.citekey}`,
+            });
+        }
+    }
+    return findings;
+}
+/**
+ * Orphaned bibliography entries (reverse linkage, H2). Informational only —
+ * `note` level, never gating. Bibliography-level finding, so uses the
+ * sources.json:0 stand-in location.
+ */
+function collectOrphanFindings(output) {
+    const findings = [];
+    for (const entry of output.linkage) {
+        if (entry.status !== 'orphan')
+            continue;
+        findings.push({
+            file: 'sources.json',
+            line: 0,
+            level: 'note',
+            message: `orphaned bibliography entry @${entry.citekey} (never cited; informational)`,
+        });
+    }
+    return findings;
+}
+function collectPhraseFlagFindings(output) {
+    const findings = [];
+    for (const flag of output.phraseFlags) {
+        if (flag.status !== 'flagged')
+            continue;
+        findings.push({
+            file: flag.file,
+            line: flag.line,
+            level: 'warning',
+            message: `phrase [${flag.patternKey}]: "${flag.matchedText}"`,
+        });
+    }
+    return findings;
+}
+function collectWorklistFindings(output) {
+    const findings = [];
+    for (const item of output.worklist) {
+        findings.push({
+            file: item.file,
+            line: item.line,
+            level: 'note',
+            message: `worklist [${item.type}] ${item.citation} — ${item.recommendedAction}`,
+        });
+    }
+    return findings;
+}
+// ---------------------------------------------------------------------------
+// Public API
+// ---------------------------------------------------------------------------
+/**
+ * Render a validated Output as a compact text string.
+ *
+ * Format: one line per finding as `<file>:<line>: <level>: <message>`,
+ * followed by a summary line with counts.
+ *
+ * Level mapping (same as SARIF):
+ * - error: existence metadata-mismatch, canonical dead-url/wrong-host/etc, linkage unresolved
+ * - warning: phrase flags (flagged, not acknowledged)
+ * - note: existence unverifiable, worklist items, orphaned bibliography entries
+ */
+export function renderText(output) {
+    const allFindings = [
+        ...collectIdentifierFindings(output),
+        ...collectExistenceFindings(output),
+        ...collectCanonicalFindings(output),
+        ...collectLinkageFindings(output),
+        ...collectOrphanFindings(output),
+        ...collectPhraseFlagFindings(output),
+        ...collectWorklistFindings(output),
+    ];
+    // Sort for determinism: file, line, level, message.
+    allFindings.sort((a, b) => {
+        const fc = a.file.localeCompare(b.file);
+        if (fc !== 0)
+            return fc;
+        if (a.line !== b.line)
+            return a.line - b.line;
+        if (a.level !== b.level)
+            return a.level.localeCompare(b.level);
+        return a.message.localeCompare(b.message);
+    });
+    const errors = allFindings.filter((f) => f.level === 'error').length;
+    const warnings = allFindings.filter((f) => f.level === 'warning').length;
+    const notes = allFindings.filter((f) => f.level === 'note').length;
+    const lines = allFindings.map(fmt);
+    lines.push(`${errors} errors, ${warnings} warnings, ${notes} notes`);
+    return lines.join('\n') + '\n';
+}
+//# sourceMappingURL=text.js.map

package/dist/output/text.js.map

@@ -0,0 +1 @@
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package/dist/phrases/load.d.ts

@@ -0,0 +1,34 @@
+/**
+ * Phrase denylist loader.
+ *
+ * Reads a project-supplied TOML file, validates it with Zod, compiles each
+ * pattern with RE2JS (linear-time guarantees; ReDoS-safe), and returns the
+ * resulting CompiledPattern[].
+ */
+import { RE2JS } from 're2js';
+export interface DenylistEntry {
+    key: string;
+    regex: string;
+    flags: string;
+    referenceUrl: string | null;
+    description?: string;
+}
+export interface CompiledPattern {
+    key: string;
+    regex: string;
+    flags: string;
+    compiled: ReturnType<typeof RE2JS.compile>;
+    referenceUrl: string | null;
+    description?: string;
+}
+export interface LoadDenylistOptions {
+    path: string;
+    cwd?: string;
+}
+export declare class PhraseLoaderError extends Error {
+    readonly cause?: unknown | undefined;
+    name: "PhraseLoaderError";
+    constructor(message: string, cause?: unknown | undefined);
+}
+export declare function loadDenylist(opts: LoadDenylistOptions): Promise<CompiledPattern[]>;
+//# sourceMappingURL=load.d.ts.map

package/dist/phrases/load.d.ts.map

@@ -0,0 +1 @@
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