scientify 2.1.0 → 3.0.0

package/dist/src/tools/scientify-literature-state.js

@@ -1,957 +0,0 @@
-import { Type } from "@sinclair/typebox";
-import { getIncrementalStateStatus, prepareIncrementalState, recordIncrementalPush, recordUserFeedback, } from "../literature/subscription-state.js";
-import { Result } from "./result.js";
-const PreferencesSchema = Type.Optional(Type.Object({
-    max_papers: Type.Optional(Type.Number({
-        description: "Maximum number of papers to push each run (1-20).",
-    })),
-    recency_days: Type.Optional(Type.Number({
-        description: "Optional recency preference in days for candidate retrieval.",
-    })),
-    sources: Type.Optional(Type.Array(Type.String({
-        description: "Preferred search sources, for example: arxiv, openalex.",
-    }))),
-}));
-const PaperSchema = Type.Object({
-    id: Type.Optional(Type.String({ description: "Stable paper id, such as arxiv:2501.12345 or doi:10.xxxx/..." })),
-    title: Type.Optional(Type.String({ description: "Paper title." })),
-    url: Type.Optional(Type.String({ description: "Source URL for traceability." })),
-    score: Type.Optional(Type.Number({
-        description: "Optional internal ranking score for backend logging (for example 0-100).",
-    })),
-    reason: Type.Optional(Type.String({
-        description: "Optional internal ranking rationale for backend logging.",
-    })),
-});
-const KnowledgePaperSchema = Type.Object({
-    id: Type.Optional(Type.String({ description: "Optional stable paper id." })),
-    title: Type.Optional(Type.String({ description: "Paper title." })),
-    url: Type.Optional(Type.String({ description: "Paper source URL." })),
-    source: Type.Optional(Type.String({ description: "Paper source name/domain." })),
-    published_at: Type.Optional(Type.String({ description: "Published time in ISO string." })),
-    score: Type.Optional(Type.Number({ description: "Optional score used in ranking." })),
-    reason: Type.Optional(Type.String({ description: "Optional rationale for selecting this paper." })),
-    summary: Type.Optional(Type.String({ description: "Optional short summary text." })),
-    evidence_ids: Type.Optional(Type.Array(Type.String({ description: "Optional evidence IDs for this paper." }))),
-    full_text_read: Type.Optional(Type.Boolean({ description: "Whether this paper was read from full text." })),
-    read_status: Type.Optional(Type.String({
-        description: "Read status: fulltext | partial | metadata | unread.",
-    })),
-    full_text_source: Type.Optional(Type.String({ description: "Where full text came from (e.g. arxiv_pdf)." })),
-    full_text_ref: Type.Optional(Type.String({ description: "Reference to full text location/path/URL." })),
-    unread_reason: Type.Optional(Type.String({ description: "Why full-text reading was not completed." })),
-    key_evidence_spans: Type.Optional(Type.Array(Type.String({ description: "Short evidence excerpts/anchors from full text." }))),
-    domain: Type.Optional(Type.String({ description: "Primary research domain." })),
-    subdomains: Type.Optional(Type.Array(Type.String({ description: "Sub-research domains." }))),
-    cross_domain_links: Type.Optional(Type.Array(Type.String({ description: "Cross-domain links/intersections." }))),
-    research_goal: Type.Optional(Type.String({ description: "Core research goal/question of this paper." })),
-    approach: Type.Optional(Type.String({ description: "What the paper does under that goal." })),
-    methodology_design: Type.Optional(Type.String({ description: "Method/experiment design summary." })),
-    key_contributions: Type.Optional(Type.Array(Type.String({ description: "Main contributions of this paper." }))),
-    practical_insights: Type.Optional(Type.Array(Type.String({ description: "Practical takeaways or reusable experience." }))),
-    must_understand_points: Type.Optional(Type.Array(Type.String({ description: "Critical points that must be understood after reading." }))),
-    limitations: Type.Optional(Type.Array(Type.String({ description: "Known limitations." }))),
-    evidence_anchors: Type.Optional(Type.Array(Type.Object({
-        section: Type.Optional(Type.String({ description: "Section title or identifier." })),
-        locator: Type.Optional(Type.String({ description: "Fine-grained locator, e.g. Eq.3/Table2/Page4." })),
-        claim: Type.String({ description: "Claim supported by this anchor." }),
-        quote: Type.Optional(Type.String({ description: "Short quote/excerpt supporting the claim." })),
-    }))),
-});
-const ExplorationTraceSchema = Type.Object({
-    query: Type.String({ description: "Exploration query text." }),
-    reason: Type.Optional(Type.String({ description: "Why this exploration query was chosen." })),
-    source: Type.Optional(Type.String({ description: "Source used for this exploration step (e.g. arxiv/openalex)." })),
-    candidates: Type.Optional(Type.Number({ description: "Candidate count before filtering." })),
-    filtered_to: Type.Optional(Type.Number({ description: "Candidate count after filtering." })),
-    filtered_out_reasons: Type.Optional(Type.Array(Type.String({ description: "Optional filtering reasons for dropped candidates." }))),
-    result_count: Type.Optional(Type.Number({ description: "Optional result count from this query." })),
-});
-const KnowledgeChangeSchema = Type.Object({
-    type: Type.String({ description: "One of NEW|CONFIRM|REVISE|BRIDGE." }),
-    statement: Type.String({ description: "Change statement." }),
-    evidence_ids: Type.Optional(Type.Array(Type.String({ description: "Evidence IDs for this change." }))),
-    topic: Type.Optional(Type.String({ description: "Optional topic affected by this change." })),
-});
-const KnowledgeUpdateSchema = Type.Object({
-    topic: Type.String({ description: "Topic name for this update." }),
-    op: Type.String({ description: "Update operation: append|revise|confirm|bridge." }),
-    content: Type.String({ description: "Update content text." }),
-    confidence: Type.Optional(Type.String({ description: "Optional confidence: low|medium|high." })),
-    evidence_ids: Type.Optional(Type.Array(Type.String({ description: "Evidence IDs for this update." }))),
-});
-const KnowledgeHypothesisSchema = Type.Object({
-    id: Type.Optional(Type.String({ description: "Optional hypothesis ID." })),
-    statement: Type.String({ description: "Hypothesis statement." }),
-    trigger: Type.String({ description: "Trigger type: GAP|BRIDGE|TREND|CONTRADICTION." }),
-    dependency_path: Type.Optional(Type.Array(Type.String({ description: "Dependency path steps." }))),
-    novelty: Type.Optional(Type.Number({ description: "Optional novelty score." })),
-    feasibility: Type.Optional(Type.Number({ description: "Optional feasibility score." })),
-    impact: Type.Optional(Type.Number({ description: "Optional impact score." })),
-    evidence_ids: Type.Optional(Type.Array(Type.String({ description: "Evidence IDs for this hypothesis." }))),
-    validation_status: Type.Optional(Type.String({
-        description: "Optional validation status: unchecked | supporting | conflicting | openreview_related | openreview_not_found.",
-    })),
-    validation_notes: Type.Optional(Type.String({ description: "Optional validation notes." })),
-    validation_evidence: Type.Optional(Type.Array(Type.String({ description: "Optional validation evidence links/ids." }))),
-});
-const KnowledgeRunLogSchema = Type.Object({
-    model: Type.Optional(Type.String({ description: "Optional model name." })),
-    duration_ms: Type.Optional(Type.Number({ description: "Optional run duration in ms." })),
-    error: Type.Optional(Type.String({ description: "Optional run error text." })),
-    degraded: Type.Optional(Type.Boolean({ description: "Whether this run used degraded behavior." })),
-    notes: Type.Optional(Type.String({ description: "Optional extra notes." })),
-    temp_full_text_dir: Type.Optional(Type.String({ description: "Temporary local directory for full-text files." })),
-    temp_files_downloaded: Type.Optional(Type.Number({ description: "Number of temporary full-text files downloaded." })),
-    temp_cleanup_status: Type.Optional(Type.String({
-        description: "Temporary full-text cleanup status: done | partial | failed | not_needed.",
-    })),
-    temp_cleanup_note: Type.Optional(Type.String({ description: "Optional cleanup note/error." })),
-    full_text_attempted: Type.Optional(Type.Number({ description: "Number of papers attempted for full-text read." })),
-    full_text_completed: Type.Optional(Type.Number({ description: "Number of papers successfully full-text read." })),
-});
-const KnowledgeStateSchema = Type.Optional(Type.Object({
-    core_papers: Type.Optional(Type.Array(KnowledgePaperSchema)),
-    exploration_papers: Type.Optional(Type.Array(KnowledgePaperSchema)),
-    exploration_trace: Type.Optional(Type.Array(ExplorationTraceSchema)),
-    knowledge_changes: Type.Optional(Type.Array(KnowledgeChangeSchema)),
-    knowledge_updates: Type.Optional(Type.Array(KnowledgeUpdateSchema)),
-    hypotheses: Type.Optional(Type.Array(KnowledgeHypothesisSchema)),
-    run_log: Type.Optional(KnowledgeRunLogSchema),
-}));
-export const ScientifyLiteratureStateToolSchema = Type.Object({
-    action: Type.String({
-        description: 'Action: "prepare" | "record" | "feedback" | "status". `status` returns recent papers plus knowledge_state summary for follow-up traceability.',
-    }),
-    scope: Type.String({
-        description: "Scope key used to isolate user/channel state.",
-    }),
-    topic: Type.String({
-        description: "Research topic text.",
-    }),
-    project_id: Type.Optional(Type.String({
-        description: "Optional project id to pin knowledge_state writes.",
-    })),
-    preferences: PreferencesSchema,
-    papers: Type.Optional(Type.Array(PaperSchema, {
-        description: "Papers to mark as pushed when action=record.",
-    })),
-    status: Type.Optional(Type.String({
-        description: "Run status for action=record, for example: ok, empty, error.",
-    })),
-    run_id: Type.Optional(Type.String({
-        description: "Optional cron run/session id for traceability.",
-    })),
-    note: Type.Optional(Type.String({
-        description: "Optional note for this record.",
-    })),
-    signal: Type.Optional(Type.String({
-        description: 'Feedback signal for action=feedback: "read" | "skip" | "star".',
-    })),
-    paper: Type.Optional(Type.Object({
-        id: Type.Optional(Type.String({ description: "Optional paper id for feedback context." })),
-        title: Type.Optional(Type.String({ description: "Optional paper title for feedback context." })),
-        url: Type.Optional(Type.String({ description: "Optional paper URL for feedback context." })),
-    })),
-    source: Type.Optional(Type.String({
-        description: "Optional source hint for feedback (e.g. arxiv/openalex/domain).",
-    })),
-    tags: Type.Optional(Type.Array(Type.String({
-        description: "Optional feedback tags, e.g. [\"physics simulation\", \"agent\"].",
-    }))),
-    knowledge_state: KnowledgeStateSchema,
-});
-function readStringParam(params, key) {
-    const value = params[key];
-    if (typeof value !== "string")
-        return undefined;
-    const trimmed = value.trim();
-    return trimmed.length > 0 ? trimmed : undefined;
-}
-function readPreferences(params) {
-    const raw = params.preferences;
-    if (!raw || typeof raw !== "object" || Array.isArray(raw))
-        return undefined;
-    const record = raw;
-    const maxRaw = record.max_papers;
-    const recencyRaw = record.recency_days;
-    const sourcesRaw = record.sources;
-    const maxPapers = typeof maxRaw === "number" && Number.isFinite(maxRaw) ? maxRaw : undefined;
-    const recencyDays = typeof recencyRaw === "number" && Number.isFinite(recencyRaw) ? recencyRaw : undefined;
-    const sources = Array.isArray(sourcesRaw) && sourcesRaw.length > 0
-        ? sourcesRaw
-            .filter((item) => typeof item === "string")
-            .map((item) => item.trim())
-            .filter((item) => item.length > 0)
-        : undefined;
-    if (maxPapers === undefined && recencyDays === undefined && (!sources || sources.length === 0)) {
-        return undefined;
-    }
-    return {
-        ...(maxPapers !== undefined ? { maxPapers } : {}),
-        ...(recencyDays !== undefined ? { recencyDays } : {}),
-        ...(sources && sources.length > 0 ? { sources } : {}),
-    };
-}
-function readPapers(params) {
-    const raw = params.papers;
-    if (!Array.isArray(raw))
-        return [];
-    const papers = [];
-    for (const item of raw) {
-        if (!item || typeof item !== "object" || Array.isArray(item))
-            continue;
-        const record = item;
-        const id = typeof record.id === "string" ? record.id.trim() : undefined;
-        const title = typeof record.title === "string" ? record.title.trim() : undefined;
-        const url = typeof record.url === "string" ? record.url.trim() : undefined;
-        const score = typeof record.score === "number" && Number.isFinite(record.score)
-            ? record.score
-            : undefined;
-        const reason = typeof record.reason === "string" ? record.reason.trim() : undefined;
-        papers.push({
-            ...(id ? { id } : {}),
-            ...(title ? { title } : {}),
-            ...(url ? { url } : {}),
-            ...(score !== undefined ? { score } : {}),
-            ...(reason ? { reason } : {}),
-        });
-    }
-    return papers;
-}
-function readFeedbackSignal(params) {
-    const raw = readStringParam(params, "signal")?.toLowerCase();
-    if (raw === "read" || raw === "skip" || raw === "star")
-        return raw;
-    return undefined;
-}
-function readFeedbackPaper(params) {
-    const raw = params.paper;
-    if (!raw || typeof raw !== "object" || Array.isArray(raw))
-        return undefined;
-    const record = raw;
-    const id = typeof record.id === "string" ? record.id.trim() : undefined;
-    const title = typeof record.title === "string" ? record.title.trim() : undefined;
-    const url = typeof record.url === "string" ? record.url.trim() : undefined;
-    if (!id && !title && !url)
-        return undefined;
-    return {
-        ...(id ? { id } : {}),
-        ...(title ? { title } : {}),
-        ...(url ? { url } : {}),
-    };
-}
-function readStringList(params, key) {
-    const raw = params[key];
-    if (!Array.isArray(raw))
-        return undefined;
-    const values = raw
-        .filter((item) => typeof item === "string")
-        .map((item) => item.trim())
-        .filter((item) => item.length > 0);
-    return values.length > 0 ? values : undefined;
-}
-function readKnowledgePapers(raw) {
-    if (!Array.isArray(raw))
-        return [];
-    const papers = [];
-    for (const item of raw) {
-        if (!item || typeof item !== "object" || Array.isArray(item))
-            continue;
-        const record = item;
-        const id = typeof record.id === "string" ? record.id.trim() : undefined;
-        const title = typeof record.title === "string" ? record.title.trim() : undefined;
-        const url = typeof record.url === "string" ? record.url.trim() : undefined;
-        const source = typeof record.source === "string" ? record.source.trim() : undefined;
-        const publishedAt = typeof record.published_at === "string"
-            ? record.published_at.trim()
-            : typeof record.publishedAt === "string"
-                ? record.publishedAt.trim()
-                : undefined;
-        const score = typeof record.score === "number" && Number.isFinite(record.score) ? record.score : undefined;
-        const reason = typeof record.reason === "string" ? record.reason.trim() : undefined;
-        const summary = typeof record.summary === "string" ? record.summary.trim() : undefined;
-        const evidenceRaw = record.evidence_ids ?? record.evidenceIds;
-        const evidenceIds = Array.isArray(evidenceRaw)
-            ? evidenceRaw
-                .filter((v) => typeof v === "string")
-                .map((v) => v.trim())
-                .filter((v) => v.length > 0)
-            : undefined;
-        const fullTextReadRaw = record.full_text_read ?? record.fullTextRead;
-        const fullTextRead = typeof fullTextReadRaw === "boolean" ? fullTextReadRaw : undefined;
-        const readStatusRaw = typeof (record.read_status ?? record.readStatus) === "string"
-            ? String(record.read_status ?? record.readStatus).trim().toLowerCase()
-            : undefined;
-        const readStatus = readStatusRaw && ["fulltext", "partial", "metadata", "unread"].includes(readStatusRaw)
-            ? readStatusRaw
-            : undefined;
-        const fullTextSource = typeof (record.full_text_source ?? record.fullTextSource) === "string"
-            ? String(record.full_text_source ?? record.fullTextSource).trim()
-            : undefined;
-        const fullTextRef = typeof (record.full_text_ref ?? record.fullTextRef) === "string"
-            ? String(record.full_text_ref ?? record.fullTextRef).trim()
-            : undefined;
-        const unreadReason = typeof (record.unread_reason ?? record.unreadReason) === "string"
-            ? String(record.unread_reason ?? record.unreadReason).trim()
-            : undefined;
-        const keyEvidenceSpansRaw = record.key_evidence_spans ?? record.keyEvidenceSpans;
-        const keyEvidenceSpans = Array.isArray(keyEvidenceSpansRaw)
-            ? keyEvidenceSpansRaw
-                .filter((v) => typeof v === "string")
-                .map((v) => v.trim())
-                .filter((v) => v.length > 0)
-            : undefined;
-        const domain = typeof record.domain === "string" ? record.domain.trim() : undefined;
-        const subdomainsRaw = record.subdomains;
-        const subdomains = Array.isArray(subdomainsRaw)
-            ? subdomainsRaw
-                .filter((v) => typeof v === "string")
-                .map((v) => v.trim())
-                .filter((v) => v.length > 0)
-            : undefined;
-        const crossDomainLinksRaw = record.cross_domain_links ?? record.crossDomainLinks;
-        const crossDomainLinks = Array.isArray(crossDomainLinksRaw)
-            ? crossDomainLinksRaw
-                .filter((v) => typeof v === "string")
-                .map((v) => v.trim())
-                .filter((v) => v.length > 0)
-            : undefined;
-        const researchGoal = typeof (record.research_goal ?? record.researchGoal) === "string"
-            ? String(record.research_goal ?? record.researchGoal).trim()
-            : undefined;
-        const approach = typeof record.approach === "string" ? record.approach.trim() : undefined;
-        const methodologyDesign = typeof (record.methodology_design ?? record.methodologyDesign) === "string"
-            ? String(record.methodology_design ?? record.methodologyDesign).trim()
-            : undefined;
-        const keyContributionsRaw = record.key_contributions ?? record.keyContributions;
-        const keyContributions = Array.isArray(keyContributionsRaw)
-            ? keyContributionsRaw
-                .filter((v) => typeof v === "string")
-                .map((v) => v.trim())
-                .filter((v) => v.length > 0)
-            : undefined;
-        const practicalInsightsRaw = record.practical_insights ?? record.practicalInsights;
-        const practicalInsights = Array.isArray(practicalInsightsRaw)
-            ? practicalInsightsRaw
-                .filter((v) => typeof v === "string")
-                .map((v) => v.trim())
-                .filter((v) => v.length > 0)
-            : undefined;
-        const mustUnderstandPointsRaw = record.must_understand_points ?? record.mustUnderstandPoints;
-        const mustUnderstandPoints = Array.isArray(mustUnderstandPointsRaw)
-            ? mustUnderstandPointsRaw
-                .filter((v) => typeof v === "string")
-                .map((v) => v.trim())
-                .filter((v) => v.length > 0)
-            : undefined;
-        const limitationsRaw = record.limitations;
-        const limitations = Array.isArray(limitationsRaw)
-            ? limitationsRaw
-                .filter((v) => typeof v === "string")
-                .map((v) => v.trim())
-                .filter((v) => v.length > 0)
-            : undefined;
-        const evidenceAnchorsRaw = record.evidence_anchors ?? record.evidenceAnchors;
-        const evidenceAnchors = Array.isArray(evidenceAnchorsRaw)
-            ? evidenceAnchorsRaw
-                .filter((v) => !!v && typeof v === "object" && !Array.isArray(v))
-                .map((anchor) => {
-                const section = typeof anchor.section === "string" ? anchor.section.trim() : undefined;
-                const locator = typeof anchor.locator === "string" ? anchor.locator.trim() : undefined;
-                const claim = typeof anchor.claim === "string" ? anchor.claim.trim() : "";
-                const quote = typeof anchor.quote === "string" ? anchor.quote.trim() : undefined;
-                if (!claim)
-                    return undefined;
-                return {
-                    ...(section ? { section } : {}),
-                    ...(locator ? { locator } : {}),
-                    claim,
-                    ...(quote ? { quote } : {}),
-                };
-            })
-                .filter((v) => Boolean(v))
-            : undefined;
-        if (!id &&
-            !title &&
-            !url &&
-            !summary &&
-            !reason &&
-            !domain &&
-            !researchGoal &&
-            !approach &&
-            !methodologyDesign &&
-            (!keyContributions || keyContributions.length === 0) &&
-            (!practicalInsights || practicalInsights.length === 0) &&
-            (!mustUnderstandPoints || mustUnderstandPoints.length === 0) &&
-            (!limitations || limitations.length === 0)) {
-            continue;
-        }
-        papers.push({
-            ...(id ? { id } : {}),
-            ...(title ? { title } : {}),
-            ...(url ? { url } : {}),
-            ...(source ? { source } : {}),
-            ...(publishedAt ? { publishedAt } : {}),
-            ...(score !== undefined ? { score } : {}),
-            ...(reason ? { reason } : {}),
-            ...(summary ? { summary } : {}),
-            ...(evidenceIds && evidenceIds.length > 0 ? { evidenceIds } : {}),
-            ...(typeof fullTextRead === "boolean" ? { fullTextRead } : {}),
-            ...(readStatus ? { readStatus } : {}),
-            ...(fullTextSource ? { fullTextSource } : {}),
-            ...(fullTextRef ? { fullTextRef } : {}),
-            ...(unreadReason ? { unreadReason } : {}),
-            ...(keyEvidenceSpans && keyEvidenceSpans.length > 0 ? { keyEvidenceSpans } : {}),
-            ...(domain ? { domain } : {}),
-            ...(subdomains && subdomains.length > 0 ? { subdomains } : {}),
-            ...(crossDomainLinks && crossDomainLinks.length > 0 ? { crossDomainLinks } : {}),
-            ...(researchGoal ? { researchGoal } : {}),
-            ...(approach ? { approach } : {}),
-            ...(methodologyDesign ? { methodologyDesign } : {}),
-            ...(keyContributions && keyContributions.length > 0 ? { keyContributions } : {}),
-            ...(practicalInsights && practicalInsights.length > 0 ? { practicalInsights } : {}),
-            ...(mustUnderstandPoints && mustUnderstandPoints.length > 0 ? { mustUnderstandPoints } : {}),
-            ...(limitations && limitations.length > 0 ? { limitations } : {}),
-            ...(evidenceAnchors && evidenceAnchors.length > 0 ? { evidenceAnchors } : {}),
-        });
-    }
-    return papers;
-}
-function readKnowledgeStatePayload(params) {
-    const raw = params.knowledge_state;
-    if (!raw || typeof raw !== "object" || Array.isArray(raw))
-        return undefined;
-    const record = raw;
-    const corePapers = readKnowledgePapers(record.core_papers ?? record.corePapers);
-    const explorationPapers = readKnowledgePapers(record.exploration_papers ?? record.explorationPapers);
-    const explorationTraceRaw = record.exploration_trace ?? record.explorationTrace;
-    const explorationTrace = Array.isArray(explorationTraceRaw)
-        ? explorationTraceRaw
-            .filter((item) => !!item && typeof item === "object" && !Array.isArray(item))
-            .map((item) => {
-            const query = typeof item.query === "string" ? item.query.trim() : "";
-            if (!query)
-                return undefined;
-            const reason = typeof item.reason === "string" ? item.reason.trim() : undefined;
-            const source = typeof item.source === "string" ? item.source.trim() : undefined;
-            const candidatesRaw = item.candidates;
-            const candidates = typeof candidatesRaw === "number" && Number.isFinite(candidatesRaw) ? candidatesRaw : undefined;
-            const filteredToRaw = item.filtered_to ?? item.filteredTo;
-            const filteredTo = typeof filteredToRaw === "number" && Number.isFinite(filteredToRaw) ? filteredToRaw : undefined;
-            const filteredOutRaw = item.filtered_out_reasons ?? item.filteredOutReasons;
-            const filteredOutReasons = Array.isArray(filteredOutRaw)
-                ? filteredOutRaw
-                    .filter((v) => typeof v === "string")
-                    .map((v) => v.trim())
-                    .filter((v) => v.length > 0)
-                : undefined;
-            const resultCountRaw = item.result_count ?? item.resultCount;
-            const resultCount = typeof resultCountRaw === "number" && Number.isFinite(resultCountRaw)
-                ? resultCountRaw
-                : undefined;
-            return {
-                query,
-                ...(reason ? { reason } : {}),
-                ...(source ? { source } : {}),
-                ...(typeof candidates === "number" ? { candidates } : {}),
-                ...(typeof filteredTo === "number" ? { filteredTo } : {}),
-                ...(filteredOutReasons && filteredOutReasons.length > 0 ? { filteredOutReasons } : {}),
-                ...(typeof resultCount === "number" ? { resultCount } : {}),
-            };
-        })
-            .filter((item) => Boolean(item))
-        : [];
-    const knowledgeChangesRaw = record.knowledge_changes ?? record.knowledgeChanges;
-    const knowledgeChanges = [];
-    if (Array.isArray(knowledgeChangesRaw)) {
-        for (const item of knowledgeChangesRaw) {
-            if (!item || typeof item !== "object" || Array.isArray(item))
-                continue;
-            const row = item;
-            const rawType = typeof row.type === "string" ? row.type.trim().toUpperCase() : "NEW";
-            const type = ["NEW", "CONFIRM", "REVISE", "BRIDGE"].includes(rawType)
-                ? rawType
-                : "NEW";
-            const statement = typeof row.statement === "string" ? row.statement.trim() : "";
-            if (!statement)
-                continue;
-            const evidenceRaw = row.evidence_ids ?? row.evidenceIds;
-            const evidenceIds = Array.isArray(evidenceRaw)
-                ? evidenceRaw
-                    .filter((v) => typeof v === "string")
-                    .map((v) => v.trim())
-                    .filter((v) => v.length > 0)
-                : undefined;
-            const topic = typeof row.topic === "string" ? row.topic.trim() : undefined;
-            knowledgeChanges.push({
-                type,
-                statement,
-                ...(evidenceIds && evidenceIds.length > 0 ? { evidenceIds } : {}),
-                ...(topic ? { topic } : {}),
-            });
-        }
-    }
-    const knowledgeUpdatesRaw = record.knowledge_updates ?? record.knowledgeUpdates;
-    const knowledgeUpdates = [];
-    if (Array.isArray(knowledgeUpdatesRaw)) {
-        for (const item of knowledgeUpdatesRaw) {
-            if (!item || typeof item !== "object" || Array.isArray(item))
-                continue;
-            const row = item;
-            const topic = typeof row.topic === "string" ? row.topic.trim() : "";
-            const rawOp = typeof row.op === "string" ? row.op.trim().toLowerCase() : "append";
-            const op = ["append", "revise", "confirm", "bridge"].includes(rawOp)
-                ? rawOp
-                : "append";
-            const content = typeof row.content === "string" ? row.content.trim() : "";
-            if (!topic || !content)
-                continue;
-            const rawConfidence = typeof row.confidence === "string" ? row.confidence.trim().toLowerCase() : undefined;
-            const confidence = rawConfidence && ["low", "medium", "high"].includes(rawConfidence)
-                ? rawConfidence
-                : undefined;
-            const evidenceRaw = row.evidence_ids ?? row.evidenceIds;
-            const evidenceIds = Array.isArray(evidenceRaw)
-                ? evidenceRaw
-                    .filter((v) => typeof v === "string")
-                    .map((v) => v.trim())
-                    .filter((v) => v.length > 0)
-                : undefined;
-            knowledgeUpdates.push({
-                topic,
-                op,
-                content,
-                ...(confidence ? { confidence } : {}),
-                ...(evidenceIds && evidenceIds.length > 0 ? { evidenceIds } : {}),
-            });
-        }
-    }
-    const hypothesesRaw = record.hypotheses;
-    const hypotheses = [];
-    if (Array.isArray(hypothesesRaw)) {
-        for (const item of hypothesesRaw) {
-            if (!item || typeof item !== "object" || Array.isArray(item))
-                continue;
-            const row = item;
-            const id = typeof row.id === "string" ? row.id.trim() : undefined;
-            const statement = typeof row.statement === "string" ? row.statement.trim() : "";
-            const rawTrigger = typeof row.trigger === "string" ? row.trigger.trim().toUpperCase() : "TREND";
-            const trigger = ["GAP", "BRIDGE", "TREND", "CONTRADICTION"].includes(rawTrigger)
-                ? rawTrigger
-                : "TREND";
-            if (!statement)
-                continue;
-            const dependencyRaw = row.dependency_path ?? row.dependencyPath;
-            const dependencyPath = Array.isArray(dependencyRaw)
-                ? dependencyRaw
-                    .filter((v) => typeof v === "string")
-                    .map((v) => v.trim())
-                    .filter((v) => v.length > 0)
-                : undefined;
-            const evidenceRaw = row.evidence_ids ?? row.evidenceIds;
-            const evidenceIds = Array.isArray(evidenceRaw)
-                ? evidenceRaw
-                    .filter((v) => typeof v === "string")
-                    .map((v) => v.trim())
-                    .filter((v) => v.length > 0)
-                : undefined;
-            const validationStatusRaw = typeof (row.validation_status ?? row.validationStatus) === "string"
-                ? String(row.validation_status ?? row.validationStatus).trim().toLowerCase()
-                : undefined;
-            const validationStatus = validationStatusRaw &&
-                ["unchecked", "supporting", "conflicting", "openreview_related", "openreview_not_found"].includes(validationStatusRaw)
-                ? validationStatusRaw
-                : undefined;
-            const validationNotes = typeof (row.validation_notes ?? row.validationNotes) === "string"
-                ? String(row.validation_notes ?? row.validationNotes).trim()
-                : undefined;
-            const validationEvidenceRaw = row.validation_evidence ?? row.validationEvidence;
-            const validationEvidence = Array.isArray(validationEvidenceRaw)
-                ? validationEvidenceRaw
-                    .filter((v) => typeof v === "string")
-                    .map((v) => v.trim())
-                    .filter((v) => v.length > 0)
-                : undefined;
-            const novelty = typeof row.novelty === "number" && Number.isFinite(row.novelty) ? row.novelty : undefined;
-            const feasibility = typeof row.feasibility === "number" && Number.isFinite(row.feasibility) ? row.feasibility : undefined;
-            const impact = typeof row.impact === "number" && Number.isFinite(row.impact) ? row.impact : undefined;
-            hypotheses.push({
-                ...(id ? { id } : {}),
-                statement,
-                trigger,
-                ...(dependencyPath && dependencyPath.length > 0 ? { dependencyPath } : {}),
-                ...(evidenceIds && evidenceIds.length > 0 ? { evidenceIds } : {}),
-                ...(validationStatus ? { validationStatus } : {}),
-                ...(validationNotes ? { validationNotes } : {}),
-                ...(validationEvidence && validationEvidence.length > 0 ? { validationEvidence } : {}),
-                ...(novelty !== undefined ? { novelty } : {}),
-                ...(feasibility !== undefined ? { feasibility } : {}),
-                ...(impact !== undefined ? { impact } : {}),
-            });
-        }
-    }
-    const runLogRaw = record.run_log ?? record.runLog;
-    const runLog = runLogRaw && typeof runLogRaw === "object" && !Array.isArray(runLogRaw)
-        ? (() => {
-            const runLogRecord = runLogRaw;
-            const model = typeof runLogRecord.model === "string" ? runLogRecord.model.trim() : undefined;
-            const durationMsRaw = runLogRecord.duration_ms ?? runLogRecord.durationMs;
-            const durationMs = typeof durationMsRaw === "number" && Number.isFinite(durationMsRaw) ? durationMsRaw : undefined;
-            const error = typeof runLogRecord.error === "string" ? runLogRecord.error.trim() : undefined;
-            const degraded = runLogRecord.degraded === true;
-            const notes = typeof runLogRecord.notes === "string" ? runLogRecord.notes.trim() : undefined;
-            const tempFullTextDir = typeof (runLogRecord.temp_full_text_dir ?? runLogRecord.tempFullTextDir) === "string"
-                ? String(runLogRecord.temp_full_text_dir ?? runLogRecord.tempFullTextDir).trim()
-                : undefined;
-            const tempFilesDownloadedRaw = runLogRecord.temp_files_downloaded ?? runLogRecord.tempFilesDownloaded;
-            const tempFilesDownloaded = typeof tempFilesDownloadedRaw === "number" && Number.isFinite(tempFilesDownloadedRaw)
-                ? tempFilesDownloadedRaw
-                : undefined;
-            const tempCleanupStatusRaw = typeof (runLogRecord.temp_cleanup_status ?? runLogRecord.tempCleanupStatus) === "string"
-                ? String(runLogRecord.temp_cleanup_status ?? runLogRecord.tempCleanupStatus).trim().toLowerCase()
-                : undefined;
-            const tempCleanupStatus = tempCleanupStatusRaw && ["done", "partial", "failed", "not_needed"].includes(tempCleanupStatusRaw)
-                ? tempCleanupStatusRaw
-                : undefined;
-            const tempCleanupNote = typeof (runLogRecord.temp_cleanup_note ?? runLogRecord.tempCleanupNote) === "string"
-                ? String(runLogRecord.temp_cleanup_note ?? runLogRecord.tempCleanupNote).trim()
-                : undefined;
-            const fullTextAttemptedRaw = runLogRecord.full_text_attempted ?? runLogRecord.fullTextAttempted;
-            const fullTextAttempted = typeof fullTextAttemptedRaw === "number" && Number.isFinite(fullTextAttemptedRaw)
-                ? fullTextAttemptedRaw
-                : undefined;
-            const fullTextCompletedRaw = runLogRecord.full_text_completed ?? runLogRecord.fullTextCompleted;
-            const fullTextCompleted = typeof fullTextCompletedRaw === "number" && Number.isFinite(fullTextCompletedRaw)
-                ? fullTextCompletedRaw
-                : undefined;
-            if (!model &&
-                durationMs === undefined &&
-                !error &&
-                !degraded &&
-                !notes &&
-                !tempFullTextDir &&
-                tempFilesDownloaded === undefined &&
-                !tempCleanupStatus &&
-                !tempCleanupNote &&
-                fullTextAttempted === undefined &&
-                fullTextCompleted === undefined) {
-                return undefined;
-            }
-            return {
-                ...(model ? { model } : {}),
-                ...(durationMs !== undefined ? { durationMs } : {}),
-                ...(error ? { error } : {}),
-                ...(degraded ? { degraded } : {}),
-                ...(notes ? { notes } : {}),
-                ...(tempFullTextDir ? { tempFullTextDir } : {}),
-                ...(tempFilesDownloaded !== undefined ? { tempFilesDownloaded } : {}),
-                ...(tempCleanupStatus ? { tempCleanupStatus } : {}),
-                ...(tempCleanupNote ? { tempCleanupNote } : {}),
-                ...(fullTextAttempted !== undefined ? { fullTextAttempted } : {}),
-                ...(fullTextCompleted !== undefined ? { fullTextCompleted } : {}),
-            };
-        })()
-        : undefined;
-    const hasAny = corePapers.length > 0 ||
-        explorationPapers.length > 0 ||
-        explorationTrace.length > 0 ||
-        knowledgeChanges.length > 0 ||
-        knowledgeUpdates.length > 0 ||
-        hypotheses.length > 0 ||
-        Boolean(runLog);
-    if (!hasAny)
-        return undefined;
-    return {
-        ...(corePapers.length > 0 ? { corePapers } : {}),
-        ...(explorationPapers.length > 0 ? { explorationPapers } : {}),
-        ...(explorationTrace.length > 0 ? { explorationTrace } : {}),
-        ...(knowledgeChanges.length > 0 ? { knowledgeChanges } : {}),
-        ...(knowledgeUpdates.length > 0 ? { knowledgeUpdates } : {}),
-        ...(hypotheses.length > 0 ? { hypotheses } : {}),
-        ...(runLog ? { runLog } : {}),
-    };
-}
-function serializeKnowledgePaper(paper) {
-    return {
-        id: paper.id ?? null,
-        title: paper.title ?? null,
-        url: paper.url ?? null,
-        source: paper.source ?? null,
-        published_at: paper.publishedAt ?? null,
-        score: paper.score ?? null,
-        reason: paper.reason ?? null,
-        summary: paper.summary ?? null,
-        evidence_ids: paper.evidenceIds ?? [],
-        full_text_read: paper.fullTextRead ?? null,
-        read_status: paper.readStatus ?? null,
-        full_text_source: paper.fullTextSource ?? null,
-        full_text_ref: paper.fullTextRef ?? null,
-        unread_reason: paper.unreadReason ?? null,
-        key_evidence_spans: paper.keyEvidenceSpans ?? [],
-        domain: paper.domain ?? null,
-        subdomains: paper.subdomains ?? [],
-        cross_domain_links: paper.crossDomainLinks ?? [],
-        research_goal: paper.researchGoal ?? null,
-        approach: paper.approach ?? null,
-        methodology_design: paper.methodologyDesign ?? null,
-        key_contributions: paper.keyContributions ?? [],
-        practical_insights: paper.practicalInsights ?? [],
-        must_understand_points: paper.mustUnderstandPoints ?? [],
-        limitations: paper.limitations ?? [],
-        evidence_anchors: (paper.evidenceAnchors ?? []).map((anchor) => ({
-            section: anchor.section ?? null,
-            locator: anchor.locator ?? null,
-            claim: anchor.claim,
-            quote: anchor.quote ?? null,
-        })),
-    };
-}
-export function createScientifyLiteratureStateTool() {
-    return {
-        label: "Scientify Literature State",
-        name: "scientify_literature_state",
-        description: "Manage incremental research state for subscriptions: prepare dedupe context, record pushed papers plus knowledge_state artifacts, persist lightweight feedback memory, and query status.",
-        parameters: ScientifyLiteratureStateToolSchema,
-        execute: async (_toolCallId, rawArgs) => {
-            const params = (rawArgs ?? {});
-            const action = (readStringParam(params, "action") ?? "").toLowerCase();
-            const scope = readStringParam(params, "scope");
-            const topic = readStringParam(params, "topic");
-            const projectId = readStringParam(params, "project_id");
-            const preferences = readPreferences(params);
-            if (!scope || !topic) {
-                return Result.err("invalid_params", "Both `scope` and `topic` are required.");
-            }
-            try {
-                if (action === "prepare") {
-                    const prepared = await prepareIncrementalState({ scope, topic, preferences });
-                    return Result.ok({
-                        action,
-                        scope: prepared.scope,
-                        topic: prepared.topic,
-                        topic_key: prepared.topicKey,
-                        preferences: {
-                            max_papers: prepared.preferences.maxPapers,
-                            recency_days: prepared.preferences.recencyDays,
-                            sources: prepared.preferences.sources,
-                        },
-                        memory_hints: {
-                            preferred_keywords: prepared.memoryHints.preferredKeywords,
-                            avoided_keywords: prepared.memoryHints.avoidedKeywords,
-                            preferred_sources: prepared.memoryHints.preferredSources,
-                            avoided_sources: prepared.memoryHints.avoidedSources,
-                            feedback_counts: prepared.memoryHints.feedbackCounts,
-                            last_feedback_at_ms: prepared.memoryHints.lastFeedbackAtMs ?? null,
-                        },
-                        exclude_paper_ids: prepared.excludePaperIds,
-                        known_paper_count: prepared.knownPaperCount,
-                        last_pushed_at_ms: prepared.lastPushedAtMs ?? null,
-                    });
-                }
-                if (action === "record") {
-                    const papers = readPapers(params);
-                    const status = readStringParam(params, "status");
-                    const runId = readStringParam(params, "run_id");
-                    const note = readStringParam(params, "note");
-                    const knowledgeState = readKnowledgeStatePayload(params);
-                    const recorded = await recordIncrementalPush({
-                        scope,
-                        topic,
-                        preferences,
-                        status,
-                        runId,
-                        note,
-                        papers,
-                        ...(projectId ? { projectId } : {}),
-                        ...(knowledgeState ? { knowledgeState } : {}),
-                    });
-                    return Result.ok({
-                        action,
-                        scope: recorded.scope,
-                        topic: recorded.topic,
-                        topic_key: recorded.topicKey,
-                        preferences: {
-                            max_papers: recorded.preferences.maxPapers,
-                            recency_days: recorded.preferences.recencyDays,
-                            sources: recorded.preferences.sources,
-                        },
-                        memory_hints: {
-                            preferred_keywords: recorded.memoryHints.preferredKeywords,
-                            avoided_keywords: recorded.memoryHints.avoidedKeywords,
-                            preferred_sources: recorded.memoryHints.preferredSources,
-                            avoided_sources: recorded.memoryHints.avoidedSources,
-                            feedback_counts: recorded.memoryHints.feedbackCounts,
-                            last_feedback_at_ms: recorded.memoryHints.lastFeedbackAtMs ?? null,
-                        },
-                        recorded_papers: recorded.recordedPapers,
-                        total_known_papers: recorded.totalKnownPapers,
-                        pushed_at_ms: recorded.pushedAtMs,
-                        project_id: recorded.projectId ?? null,
-                        knowledge_state_summary: recorded.knowledgeStateSummary
-                            ? {
-                                project_id: recorded.knowledgeStateSummary.projectId,
-                                stream_key: recorded.knowledgeStateSummary.streamKey,
-                                total_runs: recorded.knowledgeStateSummary.totalRuns,
-                                total_hypotheses: recorded.knowledgeStateSummary.totalHypotheses,
-                                knowledge_topics_count: recorded.knowledgeStateSummary.knowledgeTopicsCount,
-                                paper_notes_count: recorded.knowledgeStateSummary.paperNotesCount,
-                                recent_full_text_read_count: recorded.knowledgeStateSummary.recentFullTextReadCount,
-                                recent_not_full_text_read_count: recorded.knowledgeStateSummary.recentNotFullTextReadCount,
-                                quality_gate: {
-                                    passed: recorded.knowledgeStateSummary.qualityGate.passed,
-                                    full_text_coverage_pct: recorded.knowledgeStateSummary.qualityGate.fullTextCoveragePct,
-                                    evidence_binding_rate_pct: recorded.knowledgeStateSummary.qualityGate.evidenceBindingRatePct,
-                                    citation_error_rate_pct: recorded.knowledgeStateSummary.qualityGate.citationErrorRatePct,
-                                    reasons: recorded.knowledgeStateSummary.qualityGate.reasons,
-                                },
-                                unread_core_paper_ids: recorded.knowledgeStateSummary.unreadCorePaperIds,
-                                last_run_at_ms: recorded.knowledgeStateSummary.lastRunAtMs ?? null,
-                                last_status: recorded.knowledgeStateSummary.lastStatus ?? null,
-                                recent_papers: recorded.knowledgeStateSummary.recentPapers.map(serializeKnowledgePaper),
-                            }
-                            : null,
-                    });
-                }
-                if (action === "feedback") {
-                    const signal = readFeedbackSignal(params);
-                    if (!signal) {
-                        return Result.err("invalid_params", 'Action "feedback" requires `signal` as one of: read, skip, star.');
-                    }
-                    const runId = readStringParam(params, "run_id");
-                    const note = readStringParam(params, "note");
-                    const source = readStringParam(params, "source");
-                    const tags = readStringList(params, "tags");
-                    const paper = readFeedbackPaper(params);
-                    const feedback = await recordUserFeedback({
-                        scope,
-                        topic,
-                        preferences,
-                        feedback: {
-                            signal,
-                            ...(paper ? { paper } : {}),
-                            ...(source ? { source } : {}),
-                            ...(tags ? { tags } : {}),
-                            ...(note ? { note } : {}),
-                            ...(runId ? { runId } : {}),
-                        },
-                    });
-                    return Result.ok({
-                        action,
-                        scope: feedback.scope,
-                        topic: feedback.topic,
-                        topic_key: feedback.topicKey,
-                        signal: feedback.signal,
-                        preferences: {
-                            max_papers: feedback.preferences.maxPapers,
-                            recency_days: feedback.preferences.recencyDays,
-                            sources: feedback.preferences.sources,
-                        },
-                        memory_hints: {
-                            preferred_keywords: feedback.memoryHints.preferredKeywords,
-                            avoided_keywords: feedback.memoryHints.avoidedKeywords,
-                            preferred_sources: feedback.memoryHints.preferredSources,
-                            avoided_sources: feedback.memoryHints.avoidedSources,
-                            feedback_counts: feedback.memoryHints.feedbackCounts,
-                            last_feedback_at_ms: feedback.memoryHints.lastFeedbackAtMs ?? null,
-                        },
-                        updated_at_ms: feedback.updatedAtMs,
-                    });
-                }
-                if (action === "status") {
-                    const status = await getIncrementalStateStatus({
-                        scope,
-                        topic,
-                        ...(projectId ? { projectId } : {}),
-                    });
-                    return Result.ok({
-                        action,
-                        scope: status.scope,
-                        topic: status.topic,
-                        topic_key: status.topicKey,
-                        preferences: {
-                            max_papers: status.preferences.maxPapers,
-                            recency_days: status.preferences.recencyDays,
-                            sources: status.preferences.sources,
-                        },
-                        memory_hints: {
-                            preferred_keywords: status.memoryHints.preferredKeywords,
-                            avoided_keywords: status.memoryHints.avoidedKeywords,
-                            preferred_sources: status.memoryHints.preferredSources,
-                            avoided_sources: status.memoryHints.avoidedSources,
-                            feedback_counts: status.memoryHints.feedbackCounts,
-                            last_feedback_at_ms: status.memoryHints.lastFeedbackAtMs ?? null,
-                        },
-                        exclude_paper_ids: status.excludePaperIds,
-                        known_paper_count: status.knownPaperCount,
-                        total_runs: status.totalRuns,
-                        last_status: status.lastStatus ?? null,
-                        last_pushed_at_ms: status.lastPushedAtMs ?? null,
-                        knowledge_state_summary: status.knowledgeStateSummary
-                            ? {
-                                project_id: status.knowledgeStateSummary.projectId,
-                                stream_key: status.knowledgeStateSummary.streamKey,
-                                total_runs: status.knowledgeStateSummary.totalRuns,
-                                total_hypotheses: status.knowledgeStateSummary.totalHypotheses,
-                                knowledge_topics_count: status.knowledgeStateSummary.knowledgeTopicsCount,
-                                paper_notes_count: status.knowledgeStateSummary.paperNotesCount,
-                                recent_full_text_read_count: status.knowledgeStateSummary.recentFullTextReadCount,
-                                recent_not_full_text_read_count: status.knowledgeStateSummary.recentNotFullTextReadCount,
-                                quality_gate: {
-                                    passed: status.knowledgeStateSummary.qualityGate.passed,
-                                    full_text_coverage_pct: status.knowledgeStateSummary.qualityGate.fullTextCoveragePct,
-                                    evidence_binding_rate_pct: status.knowledgeStateSummary.qualityGate.evidenceBindingRatePct,
-                                    citation_error_rate_pct: status.knowledgeStateSummary.qualityGate.citationErrorRatePct,
-                                    reasons: status.knowledgeStateSummary.qualityGate.reasons,
-                                },
-                                unread_core_paper_ids: status.knowledgeStateSummary.unreadCorePaperIds,
-                                last_run_at_ms: status.knowledgeStateSummary.lastRunAtMs ?? null,
-                                last_status: status.knowledgeStateSummary.lastStatus ?? null,
-                                recent_papers: status.knowledgeStateSummary.recentPapers.map(serializeKnowledgePaper),
-                            }
-                            : null,
-                        recent_hypotheses: status.recentHypotheses.map((item) => ({
-                            id: item.id,
-                            statement: item.statement,
-                            trigger: item.trigger,
-                            created_at_ms: item.createdAtMs,
-                            file: item.file,
-                        })),
-                        recent_change_stats: status.recentChangeStats.map((item) => ({
-                            day: item.day,
-                            run_id: item.runId,
-                            new_count: item.newCount,
-                            confirm_count: item.confirmCount,
-                            revise_count: item.reviseCount,
-                            bridge_count: item.bridgeCount,
-                        })),
-                        last_exploration_trace: status.lastExplorationTrace.map((item) => ({
-                            query: item.query,
-                            reason: item.reason ?? null,
-                            source: item.source ?? null,
-                            candidates: item.candidates ?? null,
-                            filtered_to: item.filteredTo ?? null,
-                            filtered_out_reasons: item.filteredOutReasons ?? [],
-                            result_count: item.resultCount ?? null,
-                        })),
-                        recent_papers: status.recentPapers.map((paper) => ({
-                            id: paper.id,
-                            title: paper.title ?? null,
-                            url: paper.url ?? null,
-                            last_score: paper.lastScore ?? null,
-                            last_reason: paper.lastReason ?? null,
-                            first_pushed_at_ms: paper.firstPushedAtMs,
-                            last_pushed_at_ms: paper.lastPushedAtMs,
-                            push_count: paper.pushCount,
-                        })),
-                    });
-                }
-                return Result.err("invalid_params", 'Invalid action. Use one of: "prepare", "record", "feedback", "status".');
-            }
-            catch (error) {
-                return Result.err("runtime_error", `scientify_literature_state failed: ${error instanceof Error ? error.message : String(error)}`);
-            }
-        },
-    };
-}
-//# sourceMappingURL=scientify-literature-state.js.map