@hongmaple0820/med-scale-research-os 0.43.0

package/dist/dashboard/MedicalWorkflowData.js

@@ -0,0 +1,664 @@
+import { existsSync, readFileSync, readdirSync, statSync } from 'node:fs';
+import { join, relative, resolve } from 'node:path';
+const REPORT_EXTENSIONS = new Set(['.html', '.pdf', '.docx', '.md', '.json', '.zip']);
+export function readMedicalWorkflowDashboard(projectDir = process.cwd()) {
+    const projectRoot = resolve(projectDir);
+    const workflowRoot = join(projectRoot, 'target-research-platform');
+    const runtimeFile = join(workflowRoot, 'output', 'dashboard_runtime', 'live_status.json');
+    if (!existsSync(runtimeFile)) {
+        return {
+            available: false,
+            projectRoot,
+            runtimeFile,
+            latestUpdatedAt: null,
+            liveStatus: null,
+            business: null,
+            manuscriptQuality: null,
+            manuscriptFactCheck: null,
+            deliveryPackage: null,
+            memorySeed: null,
+            learningCandidate: null,
+            reports: [],
+            errors: ['Medical workflow runtime status file not found. Run the target research pipeline first.'],
+        };
+    }
+    const errors = [];
+    const liveStatusRaw = readJson(runtimeFile);
+    const liveStatusPrepared = liveStatusRaw ? attachDerivedStageCompletion(projectRoot, workflowRoot, liveStatusRaw) : null;
+    const liveStatus = liveStatusPrepared ? normalizeLiveStatus(projectRoot, workflowRoot, liveStatusPrepared) : null;
+    if (!liveStatus) {
+        return {
+            available: false,
+            projectRoot,
+            runtimeFile,
+            latestUpdatedAt: null,
+            liveStatus: null,
+            business: null,
+            manuscriptQuality: null,
+            manuscriptFactCheck: null,
+            deliveryPackage: null,
+            memorySeed: null,
+            learningCandidate: null,
+            reports: [],
+            errors: ['Medical workflow runtime status file exists but could not be parsed.'],
+        };
+    }
+    const business = readBusinessSnapshot(projectRoot, workflowRoot, liveStatus, errors);
+    const manuscriptQuality = readManuscriptQuality(projectRoot, workflowRoot, liveStatus);
+    const manuscriptFactCheck = readManuscriptFactCheck(projectRoot, workflowRoot, liveStatus);
+    const deliveryPackage = readDeliveryPackage(projectRoot, workflowRoot, liveStatus);
+    const memorySeed = readMemorySeed(projectRoot, workflowRoot, liveStatus, deliveryPackage);
+    const learningCandidate = readLearningCandidate(projectRoot, workflowRoot, liveStatus, deliveryPackage);
+    const reports = collectArtifactLinks(projectRoot, workflowRoot, liveStatus, memorySeed, learningCandidate);
+    return {
+        available: true,
+        projectRoot,
+        runtimeFile,
+        latestUpdatedAt: liveStatus.updated_at ?? null,
+        liveStatus,
+        business,
+        manuscriptQuality,
+        manuscriptFactCheck,
+        deliveryPackage,
+        memorySeed,
+        learningCandidate,
+        reports,
+        errors,
+    };
+}
+function attachDerivedStageCompletion(projectRoot, workflowRoot, liveStatus) {
+    const outputRoot = resolveArtifactPath(projectRoot, workflowRoot, liveStatus.output_root);
+    const target = (liveStatus.target ?? '').trim();
+    const disease = (liveStatus.disease ?? '').trim();
+    if (!outputRoot || !target || !disease)
+        return liveStatus;
+    const diseaseVariants = [...new Set([disease, disease.replace(/\s+/g, '_')])];
+    const resultPaths = {
+        stage1: [join(outputRoot, 'stage1', `${target}_stage1_results.json`)],
+        stage2: diseaseVariants.map(token => join(outputRoot, 'stage2', `${token}_stage2_results.json`)),
+        stage3: diseaseVariants.map(token => join(outputRoot, 'stage3', `${target}_${token}_stage3_results.json`)),
+        stage4: diseaseVariants.map(token => join(outputRoot, 'stage4', `${target}_${token}_stage4_results.json`)),
+    };
+    const labels = {
+        stage1: 'Stage 1 Expression',
+        stage2: 'Stage 2 Screening',
+        stage3: 'Stage 3 Deep Research',
+        stage4: 'Stage 4 Business',
+    };
+    const stages = { ...(liveStatus.stages ?? {}) };
+    for (const [stageKey, candidates] of Object.entries(resultPaths)) {
+        const found = candidates.find(file => existsSync(file));
+        if (!found)
+            continue;
+        const current = stages[stageKey] ?? {
+            label: labels[stageKey],
+            status: 'pending',
+            startedAt: null,
+            finishedAt: null,
+            metrics: {},
+            error: null,
+        };
+        if (current.status !== 'failed') {
+            stages[stageKey] = {
+                ...current,
+                label: current.label || labels[stageKey],
+                status: 'completed',
+            };
+        }
+    }
+    return {
+        ...liveStatus,
+        stages,
+    };
+}
+function normalizeLiveStatus(projectRoot, workflowRoot, liveStatus) {
+    if (liveStatus.status !== 'completed' || liveStatus.current_stage_label)
+        return liveStatus;
+    const summary = asRecord(liveStatus.summary);
+    const deliveryPackagePath = resolveArtifactPath(projectRoot, workflowRoot, liveStatus.artifacts?.delivery_package ?? toStringOrNull(summary?.delivery_package) ?? undefined);
+    if (deliveryPackagePath && existsSync(deliveryPackagePath)) {
+        return {
+            ...liveStatus,
+            current_stage_label: '\u4ea4\u4ed8\u5305\u5df2\u5c31\u7eea',
+        };
+    }
+    const completedStageCount = Object.values(liveStatus.stages ?? {})
+        .filter(stage => stage?.status === 'completed')
+        .length;
+    if (completedStageCount === 4) {
+        return {
+            ...liveStatus,
+            current_stage_label: '\u7814\u7a76\u6d41\u7a0b\u5df2\u5b8c\u6210',
+        };
+    }
+    return liveStatus;
+}
+function readManuscriptQuality(projectRoot, workflowRoot, liveStatus) {
+    const artifacts = liveStatus.artifacts ?? {};
+    const reportPath = resolveArtifactPath(projectRoot, workflowRoot, artifacts.manuscript_quality);
+    const summary = asRecord(liveStatus.summary);
+    const inlineQuality = asRecord(summary?.quality_gate);
+    if (reportPath && existsSync(reportPath)) {
+        const payload = readJson(reportPath);
+        if (payload)
+            return normalizeManuscriptQuality({ ...(inlineQuality ?? {}), ...payload }, reportPath);
+    }
+    if (inlineQuality)
+        return normalizeManuscriptQuality(inlineQuality, reportPath);
+    return reportPath
+        ? { passed: null, score: null, errors: null, warnings: null, reportPath }
+        : null;
+}
+function normalizeManuscriptQuality(value, reportPath) {
+    return {
+        passed: typeof value.passed === 'boolean' ? value.passed : null,
+        score: toNumber(value.score),
+        grade: toStringOrNull(value.grade),
+        errors: toNumber(value.errors),
+        warnings: toNumber(value.warnings),
+        reportPath,
+    };
+}
+function readManuscriptFactCheck(projectRoot, workflowRoot, liveStatus) {
+    const artifacts = liveStatus.artifacts ?? {};
+    const reportPath = resolveArtifactPath(projectRoot, workflowRoot, artifacts.manuscript_fact_check);
+    const summary = asRecord(liveStatus.summary);
+    const inlineFactCheck = asRecord(summary?.fact_check);
+    if (reportPath && existsSync(reportPath)) {
+        const payload = readJson(reportPath);
+        if (payload)
+            return normalizeManuscriptFactCheck({ ...(inlineFactCheck ?? {}), ...payload }, reportPath);
+    }
+    if (inlineFactCheck)
+        return normalizeManuscriptFactCheck(inlineFactCheck, reportPath);
+    return reportPath
+        ? {
+            passed: null,
+            score: null,
+            errors: null,
+            warnings: null,
+            claimsChecked: null,
+            unverifiedClaims: null,
+            reportPath,
+        }
+        : null;
+}
+function normalizeManuscriptFactCheck(value, reportPath) {
+    const unverified = Array.isArray(value.unverified_claims)
+        ? value.unverified_claims.length
+        : toNumber(value.unverifiedClaims);
+    return {
+        passed: typeof value.passed === 'boolean' ? value.passed : null,
+        score: toNumber(value.score),
+        errors: toNumber(value.errors),
+        warnings: toNumber(value.warnings),
+        claimsChecked: toNumber(value.claims_checked) ?? toNumber(value.claimsChecked),
+        unverifiedClaims: unverified,
+        reportPath,
+    };
+}
+function readDeliveryPackage(projectRoot, workflowRoot, liveStatus) {
+    const artifacts = liveStatus.artifacts ?? {};
+    const summary = asRecord(liveStatus.summary);
+    const rawPackagePath = artifacts.delivery_package ?? toStringOrNull(summary?.delivery_package) ?? undefined;
+    const packagePath = resolveArtifactPath(projectRoot, workflowRoot, rawPackagePath);
+    const manifestPath = resolveArtifactPath(projectRoot, workflowRoot, artifacts.delivery_manifest);
+    if (!packagePath && !manifestPath)
+        return null;
+    const exists = Boolean(packagePath && existsSync(packagePath));
+    const manifest = manifestPath && existsSync(manifestPath)
+        ? readJson(manifestPath)
+        : null;
+    const packageAudit = normalizePackageAudit(asRecord(summary?.package_audit));
+    return {
+        packagePath,
+        manifestPath,
+        exists,
+        size: exists && packagePath ? statSync(packagePath).size : null,
+        packageAudit,
+        qualityFindings: normalizeQualityFindings(manifest?.quality_findings),
+        humanReviewTodo: normalizeStringList(manifest?.human_review_todo),
+        literatureEvidence: normalizeLiteratureEvidence(asRecord(manifest?.literature)),
+        disclaimer: toStringOrNull(manifest?.disclaimer),
+    };
+}
+function readMemorySeed(projectRoot, workflowRoot, liveStatus, deliveryPackage) {
+    const artifacts = liveStatus.artifacts ?? {};
+    const summary = asRecord(liveStatus.summary);
+    const deliveryReadiness = asRecord(summary?.delivery_readiness);
+    const inlineMemorySeed = asRecord(deliveryReadiness?.memory_seed);
+    const manifestPath = deliveryPackage?.manifestPath
+        ?? resolveArtifactPath(projectRoot, workflowRoot, artifacts.delivery_manifest);
+    if (!manifestPath && !inlineMemorySeed)
+        return null;
+    const derived = deriveMemorySeedArtifacts(projectRoot, workflowRoot, manifestPath);
+    const inlineRecordPath = resolveArtifactPath(projectRoot, workflowRoot, toStringOrNull(inlineMemorySeed?.record_path) ?? undefined);
+    const inlineSummaryPath = resolveArtifactPath(projectRoot, workflowRoot, toStringOrNull(inlineMemorySeed?.summary_path) ?? undefined);
+    const recordPath = inlineRecordPath ?? derived.recordPath;
+    let summaryPath = inlineSummaryPath ?? derived.summaryPath;
+    const payload = recordPath && existsSync(recordPath)
+        ? readJson(recordPath)
+        : null;
+    const payloadSummaryPath = resolveArtifactPath(projectRoot, workflowRoot, toStringOrNull(payload?.summary_path) ?? undefined);
+    if (payloadSummaryPath)
+        summaryPath = payloadSummaryPath;
+    if (!payload && !inlineMemorySeed && !summaryPath)
+        return null;
+    return {
+        provider: toStringOrNull(payload?.provider) ?? toStringOrNull(inlineMemorySeed?.provider),
+        generatedAt: toStringOrNull(payload?.generated_at) ?? toStringOrNull(inlineMemorySeed?.generated_at),
+        recordPath: recordPath && existsSync(recordPath) ? recordPath : null,
+        summaryPath: summaryPath && existsSync(summaryPath) ? summaryPath : null,
+        recordReady: Boolean(recordPath && existsSync(recordPath)),
+        summaryReady: Boolean(summaryPath && existsSync(summaryPath)),
+        importOk: toBooleanOrNull(payload?.import_ok) ?? toBooleanOrNull(inlineMemorySeed?.import_ok),
+        sourceFileCount: toStringArray(payload?.source_files).length || toNumber(inlineMemorySeed?.source_file_count),
+        stagedFileCount: toStringArray(payload?.staged_files).length || toNumber(inlineMemorySeed?.staged_file_count),
+        missingRoles: toStringArray(payload?.missing_roles).length > 0
+            ? toStringArray(payload?.missing_roles)
+            : toStringArray(inlineMemorySeed?.missing_roles),
+        warnings: toStringArray(payload?.warnings).length > 0
+            ? toStringArray(payload?.warnings)
+            : toStringArray(inlineMemorySeed?.warnings),
+    };
+}
+function deriveMemorySeedArtifacts(projectRoot, workflowRoot, manifestPath) {
+    if (!manifestPath)
+        return { recordPath: null, summaryPath: null };
+    const manifestName = manifestPath.replace(/\\/g, '/').split('/').pop() ?? '';
+    const slug = manifestName.replace(/_delivery_manifest\.json$/i, '');
+    if (!slug)
+        return { recordPath: null, summaryPath: null };
+    const manifestDir = manifestPath.slice(0, manifestPath.length - manifestName.length).replace(/[\\/]+$/, '');
+    const recordPath = resolveArtifactPath(projectRoot, workflowRoot, `${manifestDir}/${slug}_memory_seed.json`);
+    const summaryPath = resolveArtifactPath(projectRoot, workflowRoot, `${manifestDir}/${slug}_memory_summary.md`);
+    return { recordPath, summaryPath };
+}
+function readLearningCandidate(projectRoot, workflowRoot, liveStatus, deliveryPackage) {
+    const artifacts = liveStatus.artifacts ?? {};
+    const manifestPath = deliveryPackage?.manifestPath
+        ?? resolveArtifactPath(projectRoot, workflowRoot, artifacts.delivery_manifest);
+    if (!manifestPath)
+        return null;
+    const manifestName = manifestPath.replace(/\\/g, '/').split('/').pop() ?? '';
+    const slug = manifestName.replace(/_delivery_manifest\.json$/i, '');
+    const manifestDir = manifestPath.slice(0, manifestPath.length - manifestName.length).replace(/[\\/]+$/, '');
+    const recordPath = resolveArtifactPath(projectRoot, workflowRoot, `${manifestDir}/${slug}_memory_learning_candidate.json`);
+    const summaryPath = resolveArtifactPath(projectRoot, workflowRoot, `${manifestDir}/${slug}_memory_learning_candidate.md`);
+    const payload = recordPath && existsSync(recordPath)
+        ? readJson(recordPath)
+        : null;
+    if (!payload && !summaryPath)
+        return null;
+    return {
+        candidateId: toStringOrNull(payload?.candidate_id),
+        generatedAt: toStringOrNull(payload?.generated_at),
+        recordPath: recordPath && existsSync(recordPath) ? recordPath : null,
+        summaryPath: summaryPath && existsSync(summaryPath) ? summaryPath : null,
+        candidatePath: resolveArtifactPath(projectRoot, workflowRoot, toStringOrNull(payload?.candidate_path) ?? undefined),
+        candidateMarkdownPath: resolveArtifactPath(projectRoot, workflowRoot, toStringOrNull(payload?.candidate_markdown_path) ?? undefined),
+        recordReady: Boolean(recordPath && existsSync(recordPath)),
+        summaryReady: Boolean(summaryPath && existsSync(summaryPath)),
+        recommendedAction: toStringOrNull(payload?.recommended_action),
+        promotable: Boolean(payload?.promotable),
+        brainIngestOk: toBooleanOrNull(payload?.brain_ingest_ok),
+        brainNodeId: toStringOrNull(payload?.brain_node_id),
+        warnings: toStringArray(payload?.warnings),
+    };
+}
+function normalizeQualityFindings(value) {
+    if (!Array.isArray(value))
+        return [];
+    return value
+        .map(item => asRecord(item))
+        .filter((item) => Boolean(item))
+        .map(item => ({
+        id: toStringOrNull(item.id),
+        severity: toStringOrNull(item.severity),
+        message: toStringOrNull(item.message),
+        evidence: item.evidence ?? null,
+    }));
+}
+function normalizePackageAudit(value) {
+    if (!value)
+        return null;
+    const brokenImageRefs = Array.isArray(value.broken_image_refs)
+        ? value.broken_image_refs.length
+        : toNumber(value.brokenImageRefs);
+    const brokenMarkdownRefs = Array.isArray(value.broken_markdown_refs)
+        ? value.broken_markdown_refs.length
+        : toNumber(value.brokenMarkdownRefs);
+    return {
+        passed: typeof value.passed === 'boolean' ? value.passed : null,
+        errors: toNumber(value.errors),
+        warnings: toNumber(value.warnings),
+        entryCount: toNumber(value.entry_count) ?? toNumber(value.entryCount),
+        filesChecked: toNumber(value.files_checked) ?? toNumber(value.filesChecked),
+        markdownRefsChecked: toNumber(value.markdown_refs_checked) ?? toNumber(value.markdownRefsChecked),
+        imageRefsChecked: toNumber(value.image_refs_checked) ?? toNumber(value.imageRefsChecked),
+        readmePresent: toBooleanOrNull(value.readme_present) ?? toBooleanOrNull(value.readmePresent),
+        manifestPresent: toBooleanOrNull(value.manifest_present) ?? toBooleanOrNull(value.manifestPresent),
+        brokenImageRefs,
+        brokenMarkdownRefs,
+    };
+}
+function normalizeStringList(value) {
+    if (!Array.isArray(value))
+        return [];
+    return value
+        .map(item => typeof item === 'string' ? item : null)
+        .filter((item) => Boolean(item && item.trim()));
+}
+function toStringArray(value) {
+    if (!Array.isArray(value))
+        return [];
+    return value
+        .map(item => typeof item === 'string' ? item.trim() : '')
+        .filter(Boolean);
+}
+function normalizeLiteratureEvidence(value) {
+    if (!value)
+        return null;
+    const enrichment = asRecord(value.enrichment);
+    const sources = Array.isArray(enrichment?.sources)
+        ? enrichment.sources.map(item => String(item)).filter(Boolean)
+        : [];
+    return {
+        count: toNumber(value.count),
+        agentCacheCount: toNumber(value.agent_cache_count),
+        llmCount: toNumber(value.llm_count),
+        ruleBasedCount: toNumber(value.rule_based_count),
+        sources,
+        meshCount: toNumber(enrichment?.mesh_count),
+        citationCountAvailable: toNumber(enrichment?.citation_count_available),
+        cacheUsed: typeof enrichment?.cache_used === 'boolean' ? enrichment.cache_used : null,
+        cacheHitCount: toNumber(enrichment?.cache_hit_count),
+    };
+}
+function readBusinessSnapshot(projectRoot, workflowRoot, liveStatus, errors) {
+    const artifacts = liveStatus.artifacts ?? {};
+    const preferredFiles = [
+        artifacts.stage4_json,
+        artifacts.stage4_milestones,
+    ].filter((value) => Boolean(value));
+    for (const file of preferredFiles) {
+        const absolute = resolveArtifactPath(projectRoot, workflowRoot, file);
+        if (!absolute || !existsSync(absolute))
+            continue;
+        const payload = readJson(absolute);
+        if (!payload)
+            continue;
+        const snapshot = normalizeBusinessSnapshot(payload);
+        if (snapshot)
+            return snapshot;
+    }
+    const derived = deriveBusinessArtifactCandidates(projectRoot, workflowRoot, liveStatus);
+    for (const absolute of derived) {
+        if (!existsSync(absolute))
+            continue;
+        const payload = readJson(absolute);
+        if (!payload)
+            continue;
+        const snapshot = normalizeBusinessSnapshot(payload);
+        if (snapshot)
+            return snapshot;
+    }
+    if (liveStatus.stages?.stage4?.metrics) {
+        return {
+            overallSuccessRate: toNumber(liveStatus.stages.stage4.metrics.success_rate),
+            totalDurationMonths: parseDurationMonths(liveStatus.stages.stage4.metrics.total_duration),
+            totalCostEstimate: parseCostValue(liveStatus.stages.stage4.metrics.total_cost),
+            estimatedCompletion: toStringOrNull(liveStatus.stages.stage4.metrics.estimated_completion),
+            dataSources: [],
+            adjustmentDetails: {},
+            milestones: [],
+        };
+    }
+    errors.push('Stage 4 business snapshot is not available yet.');
+    return null;
+}
+function deriveBusinessArtifactCandidates(projectRoot, workflowRoot, liveStatus) {
+    const outputRoot = resolveArtifactPath(projectRoot, workflowRoot, liveStatus.output_root);
+    const target = (liveStatus.target ?? '').trim();
+    const disease = (liveStatus.disease ?? '').trim();
+    if (!outputRoot || !target || !disease)
+        return [];
+    const diseaseVariants = [...new Set([
+            disease,
+            disease.replace(/\s+/g, '_'),
+        ])];
+    const candidates = [];
+    for (const diseaseToken of diseaseVariants) {
+        candidates.push(join(outputRoot, 'stage4', `${target}_${diseaseToken}_stage4_results.json`));
+        candidates.push(join(outputRoot, 'stage4', `${target}_${diseaseToken}_milestones.json`));
+    }
+    return candidates;
+}
+function normalizeBusinessSnapshot(payload) {
+    const container = pickBusinessContainer(payload);
+    if (!container)
+        return null;
+    const stageAdjustments = asRecord(container.stage_adjustments);
+    const adjustmentDetails = asRecord(stageAdjustments?.adjustment_details) ?? {};
+    const milestones = Array.isArray(container.milestones)
+        ? container.milestones.map(normalizeMilestone).filter((value) => Boolean(value))
+        : [];
+    return {
+        overallSuccessRate: toNumber(container.overall_success_rate),
+        totalDurationMonths: toNumber(container.total_duration_months),
+        totalCostEstimate: toNumber(container.total_cost_estimate),
+        estimatedCompletion: toStringOrNull(container.estimated_completion),
+        dataSources: Array.isArray(stageAdjustments?.data_sources)
+            ? stageAdjustments.data_sources.map(item => String(item))
+            : [],
+        adjustmentDetails,
+        milestones,
+    };
+}
+function pickBusinessContainer(payload) {
+    if (typeof payload.overall_success_rate !== 'undefined')
+        return payload;
+    const stages = asRecord(payload.stages);
+    const milestoneStage = asRecord(stages?.milestones);
+    const data = asRecord(milestoneStage?.data);
+    if (data && typeof data.overall_success_rate !== 'undefined')
+        return data;
+    return null;
+}
+function normalizeMilestone(value) {
+    const record = asRecord(value);
+    if (!record)
+        return null;
+    return {
+        phase: toStringOrNull(record.phase) ?? 'unknown',
+        phaseName: toStringOrNull(record.phase_name) ?? toStringOrNull(record.phase) ?? 'Unknown',
+        durationMonths: toNumber(record.duration_months),
+        successRate: toNumber(record.success_rate),
+        cumulativeCost: toNumber(record.cumulative_cost),
+        endDate: toStringOrNull(record.end_date),
+    };
+}
+function collectArtifactLinks(projectRoot, workflowRoot, liveStatus, memorySeed, learningCandidate) {
+    const links = new Map();
+    const knownArtifacts = liveStatus.artifacts ?? {};
+    for (const [key, file] of Object.entries(knownArtifacts)) {
+        const absolute = resolveArtifactPath(projectRoot, workflowRoot, file);
+        if (!absolute)
+            continue;
+        const exists = existsSync(absolute);
+        const kind = classifyArtifact(absolute);
+        links.set(absolute, {
+            label: prettifyArtifactLabel(key),
+            kind,
+            path: absolute,
+            relativePath: relative(projectRoot, absolute),
+            url: artifactUrl(absolute),
+            exists,
+        });
+    }
+    for (const [key, file] of [
+        ['memory_seed_record', memorySeed?.recordPath],
+        ['memory_seed_summary', memorySeed?.summaryPath],
+        ['learning_candidate_record', learningCandidate?.recordPath],
+        ['learning_candidate_summary', learningCandidate?.summaryPath],
+    ]) {
+        if (!file)
+            continue;
+        links.set(file, {
+            label: prettifyArtifactLabel(key),
+            kind: classifyArtifact(file),
+            path: file,
+            relativePath: relative(projectRoot, file),
+            url: artifactUrl(file),
+            exists: existsSync(file),
+        });
+    }
+    const outputRoot = resolveArtifactPath(projectRoot, workflowRoot, liveStatus.output_root);
+    if (outputRoot && existsSync(outputRoot)) {
+        for (const discovered of findReportFiles(outputRoot, 3, 24)) {
+            if (links.has(discovered))
+                continue;
+            links.set(discovered, {
+                label: prettifyArtifactLabel(relative(outputRoot, discovered)),
+                kind: classifyArtifact(discovered),
+                path: discovered,
+                relativePath: relative(projectRoot, discovered),
+                url: artifactUrl(discovered),
+                exists: true,
+            });
+        }
+    }
+    return [...links.values()]
+        .filter(link => link.exists)
+        .sort((left, right) => left.label.localeCompare(right.label));
+}
+function findReportFiles(root, maxDepth, maxFiles) {
+    const results = [];
+    function walk(dir, depth) {
+        if (depth > maxDepth || results.length >= maxFiles)
+            return;
+        for (const entry of readdirSync(dir, { withFileTypes: true })) {
+            if (results.length >= maxFiles)
+                return;
+            const absolute = join(dir, entry.name);
+            if (entry.isDirectory()) {
+                if (entry.name.startsWith('.'))
+                    continue;
+                walk(absolute, depth + 1);
+                continue;
+            }
+            if (!entry.isFile())
+                continue;
+            if (!isReportCandidate(entry.name))
+                continue;
+            const stats = statSync(absolute);
+            results.push({ path: absolute, mtimeMs: stats.mtimeMs });
+        }
+    }
+    walk(root, 0);
+    return results
+        .sort((left, right) => right.mtimeMs - left.mtimeMs)
+        .map(item => item.path);
+}
+function isReportCandidate(fileName) {
+    const lower = fileName.toLowerCase();
+    if (!hasReportExtension(lower))
+        return false;
+    return (lower.includes('report')
+        || lower.includes('milestone')
+        || lower.includes('pipeline_output')
+        || lower.includes('manuscript')
+        || lower.includes('memory_summary')
+        || lower.includes('memory_seed')
+        || lower.includes('learning_candidate'));
+}
+function hasReportExtension(fileName) {
+    for (const extension of REPORT_EXTENSIONS) {
+        if (fileName.endsWith(extension))
+            return true;
+    }
+    return false;
+}
+function classifyArtifact(path) {
+    const lower = path.toLowerCase();
+    if (lower.endsWith('.html'))
+        return 'html';
+    if (lower.endsWith('.pdf'))
+        return 'pdf';
+    if (lower.endsWith('.docx'))
+        return 'docx';
+    if (lower.endsWith('.md'))
+        return 'markdown';
+    if (lower.endsWith('.json'))
+        return 'json';
+    if (lower.endsWith('.zip'))
+        return 'zip';
+    return 'other';
+}
+function prettifyArtifactLabel(value) {
+    return value
+        .replace(/\\/g, ' / ')
+        .replace(/_/g, ' ')
+        .replace(/\bjson\b/gi, 'JSON')
+        .replace(/\bhtml\b/gi, 'HTML')
+        .replace(/\bpdf\b/gi, 'PDF')
+        .replace(/\bdocx\b/gi, 'DOCX');
+}
+function artifactUrl(path) {
+    return `/medical-artifact?path=${encodeURIComponent(path)}`;
+}
+function resolveArtifactPath(projectRoot, workflowRoot, rawPath) {
+    if (!rawPath)
+        return null;
+    if (/^[A-Za-z]:[\\/]/.test(rawPath))
+        return resolve(rawPath);
+    const workflowCandidate = resolve(workflowRoot, rawPath);
+    if (existsSync(workflowCandidate))
+        return workflowCandidate;
+    return resolve(projectRoot, rawPath);
+}
+function readJson(path) {
+    try {
+        return JSON.parse(readFileSync(path, 'utf-8'));
+    }
+    catch {
+        return null;
+    }
+}
+function asRecord(value) {
+    return value && typeof value === 'object' && !Array.isArray(value)
+        ? value
+        : null;
+}
+function toNumber(value) {
+    if (typeof value === 'number' && Number.isFinite(value))
+        return value;
+    if (typeof value === 'string') {
+        const numeric = Number(value);
+        return Number.isFinite(numeric) ? numeric : null;
+    }
+    return null;
+}
+function toStringOrNull(value) {
+    return typeof value === 'string' && value.length > 0 ? value : null;
+}
+function toBooleanOrNull(value) {
+    return typeof value === 'boolean' ? value : null;
+}
+function parseDurationMonths(value) {
+    if (typeof value === 'number')
+        return value;
+    if (typeof value !== 'string')
+        return null;
+    const match = value.match(/(\d+(?:\.\d+)?)/);
+    return match ? Number(match[1]) : null;
+}
+function parseCostValue(value) {
+    if (typeof value === 'number')
+        return value;
+    if (typeof value !== 'string')
+        return null;
+    const match = value.match(/(\d+(?:\.\d+)?)/);
+    return match ? Number(match[1]) : null;
+}
+//# sourceMappingURL=MedicalWorkflowData.js.map