@alisio/plugin-thesis 0.1.0

package/dist/policy/ethics.js

@@ -0,0 +1,106 @@
+export const ethicsQuestions = [
+    {
+        id: "human_participants",
+        question: "Will human participants take part (surveys, interviews, observation, experiments)?",
+    },
+    {
+        id: "minors",
+        question: "Will children or adolescents (minors) take part, or will their data be used?",
+    },
+    {
+        id: "identifiable_personal_data",
+        question: "Will you collect or process identifiable personal data?",
+    },
+    {
+        id: "sensitive_data",
+        question: "Will you handle sensitive data (health, ethnicity, beliefs, biometrics)?",
+    },
+    {
+        id: "intervention",
+        question: "Does the study include an intervention or manipulation applied to participants?",
+    },
+    { id: "risk_above_minimal", question: "Could participants face more than minimal risk?" },
+    { id: "biological_samples", question: "Will you collect or analyze biological samples?" },
+    { id: "animals", question: "Will animals be used?" },
+    {
+        id: "communities",
+        question: "Does the work involve indigenous, ethnic or other protected communities?",
+    },
+    { id: "clinical_research", question: "Is this clinical research?" },
+    {
+        id: "additional_institutional_rules",
+        question: "Does your institution add ethics rules beyond the law?",
+    },
+];
+const triggerIds = ethicsQuestions.map((question) => question.id);
+export function validateEthicsAnswers(raw) {
+    const answers = {};
+    const errors = [];
+    if (typeof raw !== "object" || raw === null || Array.isArray(raw)) {
+        return { answers, errors: ["Ethics answers must be a mapping of trigger id to true or false"] };
+    }
+    for (const [key, value] of Object.entries(raw)) {
+        if (!triggerIds.includes(key)) {
+            errors.push(`Unknown ethics trigger: ${key}`);
+        }
+        else if (typeof value !== "boolean") {
+            errors.push(`Ethics answer ${key} must be true or false`);
+        }
+        else {
+            answers[key] = value;
+        }
+    }
+    return { answers, errors };
+}
+/** Map each `yes` answer to the `ethics_trigger` rules of the resolved compliance profile. */
+export function mapEthicsRequirements(answers, profile) {
+    const requirements = [];
+    const unmapped = [];
+    const unanswered = [];
+    for (const { id } of ethicsQuestions) {
+        const answer = answers[id];
+        if (answer === undefined) {
+            unanswered.push(id);
+            continue;
+        }
+        if (!answer)
+            continue;
+        const rules = profile.rules
+            .filter((rule) => rule.kind === "ethics_trigger" && rule.values.trigger === id)
+            .sort((a, b) => (a.ruleId < b.ruleId ? -1 : 1));
+        if (rules.length === 0) {
+            unmapped.push(id);
+            requirements.push({
+                id: `ETH-${id.toUpperCase()}-00`,
+                trigger: id,
+                ruleId: null,
+                text: `No policy rule covers "${id}". Ask your institution's ethics committee which approvals and documents are required. Never assume consent is unnecessary: only an ethics committee can waive it.`,
+                requires: [],
+                generic: true,
+            });
+            continue;
+        }
+        rules.forEach((rule, index) => {
+            const values = rule.values;
+            const pick = (key) => typeof values[key] === "string" ? values[key] : undefined;
+            const text = (pick("requirement") ??
+                pick("quote") ??
+                pick("definition") ??
+                rule.source.reference).slice(0, 400);
+            const requires = Array.isArray(values.requires)
+                ? values.requires.filter((entry) => typeof entry === "string")
+                : [];
+            requirements.push({
+                id: `ETH-${id.toUpperCase()}-${String(index + 1).padStart(2, "0")}`,
+                trigger: id,
+                ruleId: rule.ruleId,
+                text,
+                requires,
+                generic: false,
+            });
+        });
+    }
+    requirements.sort((a, b) => (a.id < b.id ? -1 : 1));
+    return { requirements, unmapped, unanswered };
+}
+//# sourceMappingURL=ethics.js.map

package/dist/policy/ethics.js.map

@@ -0,0 +1 @@
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package/dist/policy/kinds.d.ts

@@ -0,0 +1,9 @@
+/** Closed `requirement.kind` vocabulary (spec section 16.2). Format-neutral by design. */
+export declare const requirementKinds: readonly ["institutional_authority", "paper", "page_margins", "font", "line_spacing", "text_alignment", "pagination", "front_matter_order", "required_section", "heading_format", "caption_position", "citation_style", "reference_format", "length_limit", "ethics_trigger", "risk_classification", "consent_requirement", "data_protection", "quotation_rule", "attribution_rule", "integrity_rule", "ai_declaration", "source_quality", "evidence_minimum", "reporting_guideline", "objective_verbs", "official_domain_allowlist", "presentation_standard"];
+export declare function isExtensionKind(kind: string): boolean;
+export declare function isKnownKind(kind: string): boolean;
+/** `appliesWhen` keys (spec section 16.2). */
+export declare const appliesWhenKeys: readonly ["country", "language", "workType", "approach", "studyDesign", "domain", "presentationStandard", "citationStyle", "ethicsTrigger", "aiUse"];
+/** Kinds that have a single resolved value; same-precedence disagreements are PCK-003. */
+export declare const exclusiveKinds: Set<string>;
+//# sourceMappingURL=kinds.d.ts.map

package/dist/policy/kinds.d.ts.map

@@ -0,0 +1 @@
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package/dist/policy/kinds.js

@@ -0,0 +1,68 @@
+/** Closed `requirement.kind` vocabulary (spec section 16.2). Format-neutral by design. */
+export const requirementKinds = [
+    "institutional_authority",
+    "paper",
+    "page_margins",
+    "font",
+    "line_spacing",
+    "text_alignment",
+    "pagination",
+    "front_matter_order",
+    "required_section",
+    "heading_format",
+    "caption_position",
+    "citation_style",
+    "reference_format",
+    "length_limit",
+    "ethics_trigger",
+    "risk_classification",
+    "consent_requirement",
+    "data_protection",
+    "quotation_rule",
+    "attribution_rule",
+    "integrity_rule",
+    "ai_declaration",
+    "source_quality",
+    "evidence_minimum",
+    "reporting_guideline",
+    "objective_verbs",
+    "official_domain_allowlist",
+    // Needed by the resolver for the selected presentation (spec section 11.3).
+    "presentation_standard",
+];
+const extensionKind = /^x-[a-z][a-z0-9-]{1,40}$/;
+export function isExtensionKind(kind) {
+    return extensionKind.test(kind);
+}
+export function isKnownKind(kind) {
+    return requirementKinds.includes(kind) || isExtensionKind(kind);
+}
+/** `appliesWhen` keys (spec section 16.2). */
+export const appliesWhenKeys = [
+    "country",
+    "language",
+    "workType",
+    "approach",
+    "studyDesign",
+    "domain",
+    "presentationStandard",
+    "citationStyle",
+    "ethicsTrigger",
+    "aiUse",
+];
+/** Kinds that have a single resolved value; same-precedence disagreements are PCK-003. */
+export const exclusiveKinds = new Set([
+    "citation_style",
+    "presentation_standard",
+    "ai_declaration",
+    "paper",
+    "page_margins",
+    "font",
+    "line_spacing",
+    "text_alignment",
+    "pagination",
+    "front_matter_order",
+    "heading_format",
+    "caption_position",
+]);
+//# sourceMappingURL=kinds.js.map

package/dist/policy/kinds.js.map

@@ -0,0 +1 @@
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package/dist/policy/packs.d.ts

@@ -0,0 +1,53 @@
+import type { Brief } from "../types.js";
+import { type LoadedRule, type PackProblem, type PackScope } from "./rules.js";
+export interface PackManifest {
+    packId: string;
+    scope: PackScope;
+    version: string;
+    appliesWhen?: Record<string, unknown>;
+    extends?: string;
+    description?: string;
+    maintainer?: string;
+    /** Optional ISO country code for country packs whose packId is not the code itself. */
+    country?: string;
+    files?: string[];
+}
+export type PackLocation = "shipped" | "workspace";
+export interface LoadedPack {
+    id: string;
+    scope: PackScope;
+    version: string;
+    location: PackLocation;
+    /** Directory name, used to match institution, faculty and program slugs. */
+    slug: string;
+    /** Directory relative to its packs root. */
+    dir: string;
+    manifest: PackManifest;
+    rules: LoadedRule[];
+}
+export declare function parseManifest(raw: unknown): {
+    manifest?: PackManifest;
+    errors: string[];
+};
+/**
+ * One loader for shipped and workspace packs; only the root directory and the location label
+ * differ. Every directory that holds a manifest.yaml is a pack.
+ */
+export declare function loadPacks(root: string, location: PackLocation): Promise<{
+    packs: LoadedPack[];
+    problems: PackProblem[];
+}>;
+/** Cross-pack validation: packId and ruleId collisions, unknown `extends`, stray `overrides`. */
+export declare function crossValidate(packs: readonly LoadedPack[]): PackProblem[];
+export interface PackSelection {
+    active: LoadedPack[];
+    inactive: {
+        packId: string;
+        location: PackLocation;
+        reason: string;
+    }[];
+    problems: PackProblem[];
+}
+/** Decide which packs apply to a brief. Pure; never depends on load order. */
+export declare function selectPacks(all: readonly LoadedPack[], brief: Brief): PackSelection;
+//# sourceMappingURL=packs.d.ts.map

package/dist/policy/packs.d.ts.map

@@ -0,0 +1 @@
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package/dist/policy/packs.js

@@ -0,0 +1,336 @@
+import { readdir } from "node:fs/promises";
+import { basename, join } from "node:path";
+import { parse } from "yaml";
+import { briefContext, matchesWhen, slugify } from "./context.js";
+import { isRecord, listYaml, packScopes, parseRuleFile, readCapped, relativeTo, } from "./rules.js";
+const packIdPattern = /^[A-Za-z0-9][A-Za-z0-9._-]{0,60}$/;
+export function parseManifest(raw) {
+    const errors = [];
+    if (!isRecord(raw))
+        return { errors: ["manifest.yaml must be a mapping"] };
+    if (typeof raw.packId !== "string" || !packIdPattern.test(raw.packId))
+        errors.push("packId is required (letters, digits, dot, dash)");
+    if (typeof raw.scope !== "string" || !packScopes.includes(raw.scope)) {
+        errors.push(`scope is required and must be one of: ${packScopes.join(", ")}`);
+    }
+    if (typeof raw.version !== "string" && typeof raw.version !== "number")
+        errors.push("version is required");
+    if (raw.appliesWhen !== undefined && !isRecord(raw.appliesWhen))
+        errors.push("appliesWhen must be a mapping");
+    if (raw.extends !== undefined &&
+        (typeof raw.extends !== "string" || !packIdPattern.test(raw.extends))) {
+        errors.push("extends must be a packId");
+    }
+    if (raw.country !== undefined &&
+        (typeof raw.country !== "string" || !/^[A-Z]{2}$/.test(raw.country))) {
+        errors.push("country must be an ISO 3166-1 alpha-2 code");
+    }
+    if (raw.files !== undefined) {
+        if (!Array.isArray(raw.files) ||
+            !raw.files.every((file) => typeof file === "string" &&
+                file &&
+                !file.startsWith("/") &&
+                !file.includes("..") &&
+                !file.includes("\\"))) {
+            errors.push("files must be a list of relative paths");
+        }
+    }
+    if (errors.length > 0)
+        return { errors };
+    return {
+        errors,
+        manifest: {
+            packId: raw.packId,
+            scope: raw.scope,
+            version: String(raw.version),
+            ...(isRecord(raw.appliesWhen) ? { appliesWhen: raw.appliesWhen } : {}),
+            ...(typeof raw.extends === "string" ? { extends: raw.extends } : {}),
+            ...(typeof raw.description === "string" ? { description: raw.description } : {}),
+            ...(typeof raw.maintainer === "string" ? { maintainer: raw.maintainer } : {}),
+            ...(typeof raw.country === "string" ? { country: raw.country } : {}),
+            ...(Array.isArray(raw.files) ? { files: raw.files } : {}),
+        },
+    };
+}
+async function findPackDirectories(root, depth = 0) {
+    let entries;
+    try {
+        entries = await readdir(root, { withFileTypes: true });
+    }
+    catch (error) {
+        if (error.code === "ENOENT")
+            return [];
+        throw error;
+    }
+    if (entries.some((entry) => entry.isFile() && entry.name === "manifest.yaml"))
+        return [root];
+    if (depth >= 6)
+        return [];
+    const found = [];
+    for (const entry of entries
+        .filter((item) => item.isDirectory())
+        .sort((a, b) => (a.name < b.name ? -1 : 1))) {
+        found.push(...(await findPackDirectories(join(root, entry.name), depth + 1)));
+    }
+    return found;
+}
+function pathScopes(relativeInsidePack) {
+    const parts = relativeInsidePack.split("/");
+    const result = {};
+    parts.forEach((part, index) => {
+        if (part === "faculties" && parts[index + 1])
+            result.faculty = parts[index + 1];
+        if (part === "programs" && parts[index + 1])
+            result.program = parts[index + 1];
+    });
+    return result;
+}
+/**
+ * One loader for shipped and workspace packs; only the root directory and the location label
+ * differ. Every directory that holds a manifest.yaml is a pack.
+ */
+export async function loadPacks(root, location) {
+    const packs = [];
+    const problems = [];
+    const prefix = location === "workspace" ? "policy-packs/" : "";
+    for (const directory of await findPackDirectories(root)) {
+        const dir = relativeTo(root, directory) || basename(directory);
+        const manifestFile = `${prefix}${dir}/manifest.yaml`;
+        let raw;
+        try {
+            raw = parse(await readCapped(join(directory, "manifest.yaml")));
+        }
+        catch (error) {
+            problems.push({
+                code: "PCK-001",
+                severity: "error",
+                file: manifestFile,
+                message: `manifest.yaml is unreadable: ${error instanceof Error ? (error.message.split("\n")[0] ?? "error") : "error"}`,
+            });
+            continue;
+        }
+        const { manifest, errors } = parseManifest(raw);
+        for (const message of errors)
+            problems.push({ code: "PCK-001", severity: "error", file: manifestFile, message });
+        if (!manifest)
+            continue;
+        const rules = [];
+        const seen = new Set();
+        const files = (await listYaml(directory, true)).filter((file) => basename(file) !== "manifest.yaml");
+        for (const absolute of files) {
+            const inside = relativeTo(directory, absolute);
+            const file = `${prefix}${dir}/${inside}`;
+            let text;
+            try {
+                text = await readCapped(absolute);
+            }
+            catch (error) {
+                problems.push({
+                    code: "PCK-001",
+                    severity: "error",
+                    file,
+                    message: error instanceof Error ? error.message : "Unreadable file",
+                });
+                continue;
+            }
+            const parsed = parseRuleFile(text, {
+                tier: "pack",
+                packId: manifest.packId,
+                scope: manifest.scope,
+                location,
+                file,
+                ...pathScopes(inside),
+            });
+            problems.push(...parsed.problems);
+            for (const rule of parsed.rules) {
+                if (seen.has(rule.ruleId)) {
+                    problems.push({
+                        code: "PCK-001",
+                        severity: "error",
+                        file,
+                        message: `Duplicate ruleId ${rule.ruleId} in pack ${manifest.packId}`,
+                    });
+                    continue;
+                }
+                seen.add(rule.ruleId);
+                rules.push(rule);
+            }
+        }
+        for (const listed of manifest.files ?? []) {
+            if (!files.some((absolute) => relativeTo(directory, absolute) === listed)) {
+                problems.push({
+                    code: "PCK-001",
+                    severity: "error",
+                    file: manifestFile,
+                    message: `Listed file ${listed} does not exist`,
+                });
+            }
+        }
+        packs.push({
+            id: manifest.packId,
+            scope: manifest.scope,
+            version: manifest.version,
+            location,
+            slug: basename(directory),
+            dir,
+            manifest,
+            rules,
+        });
+    }
+    return { packs, problems };
+}
+/** Cross-pack validation: packId and ruleId collisions, unknown `extends`, stray `overrides`. */
+export function crossValidate(packs) {
+    const problems = [];
+    const ordered = [...packs].sort((a, b) => Number(a.location === "workspace") - Number(b.location === "workspace") ||
+        (a.dir < b.dir ? -1 : 1));
+    const ids = new Map();
+    for (const pack of ordered) {
+        const prefix = pack.location === "workspace" ? "policy-packs/" : "";
+        const first = ids.get(pack.id);
+        if (first) {
+            problems.push({
+                code: "PCK-001",
+                severity: "error",
+                file: `${prefix}${pack.dir}/manifest.yaml`,
+                message: `packId ${pack.id} is already used by ${first.location === "workspace" ? "policy-packs/" : ""}${first.dir}; use extends to add rules to an existing pack`,
+            });
+        }
+        else
+            ids.set(pack.id, pack);
+    }
+    for (const pack of ordered) {
+        const target = pack.manifest.extends;
+        if (target && !ids.has(target)) {
+            problems.push({
+                code: "PCK-001",
+                severity: "error",
+                file: `${pack.location === "workspace" ? "policy-packs/" : ""}${pack.dir}/manifest.yaml`,
+                message: `extends refers to unknown pack ${target}`,
+            });
+        }
+    }
+    const definitions = new Map();
+    for (const pack of ordered) {
+        for (const rule of pack.rules)
+            definitions.set(rule.ruleId, [...(definitions.get(rule.ruleId) ?? []), rule]);
+    }
+    for (const [ruleId, list] of [...definitions.entries()].sort()) {
+        const [first, ...rest] = list;
+        if (rest.length === 0) {
+            if (first.overrides) {
+                problems.push({
+                    code: "PCK-002",
+                    severity: "error",
+                    file: first.origin.file,
+                    message: `${ruleId} sets overrides: true but no other rule has this ruleId`,
+                });
+            }
+            continue;
+        }
+        for (const later of rest) {
+            if (!later.overrides) {
+                problems.push({
+                    code: "PCK-002",
+                    severity: "error",
+                    file: later.origin.file,
+                    message: `${ruleId} is already defined in ${first.origin.file}; add overrides: true to replace it deliberately, or choose another ruleId`,
+                });
+            }
+        }
+    }
+    return problems;
+}
+/** Decide which packs apply to a brief. Pure; never depends on load order. */
+export function selectPacks(all, brief) {
+    const context = briefContext(brief);
+    const institution = slugify(brief.institution.name ?? "");
+    const faculty = slugify(brief.institution.faculty ?? "");
+    const program = slugify(brief.institution.program ?? "");
+    const setting = brief.policy.packs;
+    const problems = [];
+    const reasons = new Map();
+    if (setting !== "auto") {
+        for (const id of setting) {
+            if (!all.some((pack) => pack.id === id)) {
+                problems.push({
+                    code: "PCK-001",
+                    severity: "error",
+                    file: "thesis.yaml",
+                    message: `policy.packs lists unknown pack ${id}`,
+                });
+            }
+        }
+    }
+    const directMatch = (pack) => {
+        if (pack.scope === "global")
+            return undefined;
+        if (setting !== "auto")
+            return setting.includes(pack.id) ? undefined : "not listed in policy.packs";
+        const when = matchesWhen(pack.manifest.appliesWhen, context);
+        if (!when.ok)
+            return when.unknownKey
+                ? `unknown appliesWhen key ${when.unknownKey}`
+                : "appliesWhen does not match the brief";
+        switch (pack.scope) {
+            case "country": {
+                const country = pack.manifest.country ?? (/^[A-Z]{2}$/.test(pack.id) ? pack.id : undefined);
+                if (pack.manifest.appliesWhen?.country === undefined &&
+                    country !== undefined &&
+                    country !== brief.institution.country) {
+                    return `country pack ${country} does not match ${brief.institution.country}`;
+                }
+                return undefined;
+            }
+            case "institution":
+                return pack.slug === institution ? undefined : "institution does not match";
+            case "faculty":
+                return pack.slug === faculty ? undefined : "faculty does not match";
+            case "program":
+                return pack.slug === program ? undefined : "program does not match";
+            default:
+                return undefined;
+        }
+    };
+    const active = new Set();
+    for (const pack of all)
+        if (pack.scope === "global" || directMatch(pack) === undefined)
+            active.add(pack.id);
+    for (const pack of all) {
+        const reason = directMatch(pack);
+        if (reason)
+            reasons.set(pack.id, reason);
+    }
+    // A pack that extends another is only active while its base is.
+    for (let pass = 0; pass < all.length; pass += 1) {
+        let changed = false;
+        for (const pack of all) {
+            const base = pack.manifest.extends;
+            if (active.has(pack.id) && base && !active.has(base)) {
+                active.delete(pack.id);
+                reasons.set(pack.id, `extends ${base}, which is not active`);
+                changed = true;
+            }
+        }
+        if (!changed)
+            break;
+    }
+    const selected = [];
+    const inactive = [];
+    for (const pack of [...all].sort((a, b) => (a.id < b.id ? -1 : 1))) {
+        if (!active.has(pack.id)) {
+            inactive.push({
+                packId: pack.id,
+                location: pack.location,
+                reason: reasons.get(pack.id) ?? "not selected",
+            });
+            continue;
+        }
+        // Faculty and program sub-folders of an institution pack apply only to that faculty/program.
+        const rules = pack.rules.filter((rule) => (rule.origin.faculty === undefined || rule.origin.faculty === faculty) &&
+            (rule.origin.program === undefined || rule.origin.program === program));
+        selected.push({ ...pack, rules });
+    }
+    return { active: selected, inactive, problems };
+}
+//# sourceMappingURL=packs.js.map

package/dist/policy/packs.js.map

@@ -0,0 +1 @@
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