@gyoungwe/research-suite 0.1.5 → 0.1.6

package/node_modules/@gyoungwe/pi-research/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "@gyoungwe/pi-research",
-	"version": "0.1.0",
+	"version": "0.1.1",
 	"description": "Evidence-gated research retrieval, reading, deposition and source-grounded answer tools for native Pi",
 	"keywords": [
 		"pi-package",

package/node_modules/@gyoungwe/plugin-api/dist/index.d.ts

@@ -143,4 +143,105 @@ export interface DroneHostPort {
     runCompute(input: ComputeRequest): Promise<ComputeReceipt>;
     requestAuthorization(input: AuthorizationRequest): Promise<AuthorizationReceipt>;
 }
+export * from "./knowledge.js";
+/** Public, host-neutral analysis contract used by native Pi packages. */
+export declare const ANALYSIS_CONTRACT_VERSION: 1;
+export type AnalysisMode = "exploratory" | "inferential";
+export type AnalysisDomain = "bioinformatics" | "genomics" | "transcriptomics" | "proteomics" | "other";
+export type AnalysisResearchStage = "design" | "readiness" | "execution" | "review" | "delivery";
+export type AnalysisSideEffect = "read-only" | "network" | "project-write" | "code-execution" | "external-service";
+export type AnalysisGateSeverity = "pause" | "block";
+export type AnalysisGateCode = "scientific-ambiguity" | "missing-data" | "missing-biological-replicates" | "reference-mismatch" | "unsupported-method";
+export interface AnalysisIdentity {
+    readonly id: string;
+    readonly version: string;
+}
+export interface AnalysisGate {
+    readonly code: AnalysisGateCode;
+    readonly severity: AnalysisGateSeverity;
+    readonly message: string;
+    readonly evidenceKey: string;
+}
+export interface AnalysisReadiness {
+    readonly ok: boolean;
+    readonly inferentialClaimsAllowed: boolean;
+    readonly gates: readonly AnalysisGate[];
+    readonly warnings: readonly string[];
+}
+export interface AnalysisContext {
+    readonly version: typeof ANALYSIS_CONTRACT_VERSION;
+    readonly id: string;
+    readonly question: string;
+    readonly assay: string;
+    readonly mode: AnalysisMode;
+    readonly adapter?: AnalysisIdentity;
+}
+export interface AnalysisSchemaField {
+    readonly id: string;
+    readonly type: "file" | "table" | "metadata" | "metric" | "report";
+    readonly required: boolean;
+    readonly formats?: readonly string[];
+}
+export interface AnalysisDatasetFileRef {
+    readonly path: string;
+    readonly bytes?: number;
+    readonly sha256?: string;
+}
+/** Host maps its ComputePreflightJobSpec into this immutable portable shape. */
+export interface AnalysisComputePlanInput {
+    readonly outputs?: readonly (string | {
+        readonly path: string;
+    })[];
+    readonly dataDesign?: {
+        readonly rows?: readonly Readonly<Record<string, unknown>>[];
+        readonly dataset?: {
+            readonly files?: readonly AnalysisDatasetFileRef[];
+        };
+    };
+}
+export interface AnalysisAdapterContract {
+    readonly schemaVersion: typeof ANALYSIS_CONTRACT_VERSION;
+    readonly assay: string;
+    readonly domain: AnalysisDomain;
+    readonly researchStages: readonly AnalysisResearchStage[];
+    readonly inputs: readonly AnalysisSchemaField[];
+    readonly outputs: readonly AnalysisSchemaField[];
+    readonly capabilities: readonly string[];
+    readonly sideEffects: readonly AnalysisSideEffect[];
+    readonly evidenceTypes: readonly string[];
+    readonly workflow?: AnalysisIdentity;
+}
+export interface AnalysisArtifactEvidence {
+    readonly path: string;
+    readonly bytes?: number;
+    readonly sha256?: string;
+    readonly text?: string;
+}
+export interface AnalysisReviewCheck {
+    readonly id: string;
+    readonly passed: boolean;
+    readonly detail: string;
+}
+export interface AnalysisAdapterPlan {
+    readonly method: AnalysisIdentity;
+    readonly requiredOutputs: readonly string[];
+    readonly assessment: AnalysisReadiness;
+    readonly adapterSnapshotSha256: string;
+}
+export interface AnalysisAdapter {
+    readonly identity: AnalysisIdentity;
+    readonly contract: AnalysisAdapterContract;
+    supports(assay: string): boolean;
+    buildPlan(context: AnalysisContext, spec: AnalysisComputePlanInput, evidence: unknown): AnalysisAdapterPlan;
+    reviewResults(context: AnalysisContext, artifacts: readonly AnalysisArtifactEvidence[]): readonly AnalysisReviewCheck[];
+    readonly reviewInstructions: string;
+}
+export declare function analysisAdapterSnapshotSha256(adapter: Pick<AnalysisAdapter, "identity" | "contract">): string;
+export declare function createAnalysisContext(input: {
+    id: string;
+    question: string;
+    assay: string;
+    mode: AnalysisMode;
+    adapter: AnalysisIdentity;
+}): AnalysisContext;
 //# sourceMappingURL=index.d.ts.map

package/node_modules/@gyoungwe/plugin-api/dist/index.d.ts.map

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package/node_modules/@gyoungwe/plugin-api/dist/index.js

@@ -83,4 +83,128 @@ export function negotiateCapabilities(requirements, host) {
         missingCapabilities: [],
     };
 }
+export * from "./knowledge.js";
+/** Public, host-neutral analysis contract used by native Pi packages. */
+export const ANALYSIS_CONTRACT_VERSION = 1;
+function stableContractJson(value) {
+    if (value === null || typeof value !== "object")
+        return JSON.stringify(value) ?? "null";
+    if (Array.isArray(value))
+        return `[${value.map(stableContractJson).join(",")}]`;
+    const object = value;
+    return `{${Object.keys(object)
+        .sort()
+        .map((key) => `${JSON.stringify(key)}:${stableContractJson(object[key])}`)
+        .join(",")}}`;
+}
+// Small dependency-free SHA-256 implementation keeps the public contract
+// usable from native Pi, Electron preload and browser-based hosts alike.
+function sha256Hex(input) {
+    const encoded = encodeURIComponent(input);
+    const utf8 = [];
+    for (let i = 0; i < encoded.length; i += 1) {
+        if (encoded[i] === "%") {
+            utf8.push(Number.parseInt(encoded.slice(i + 1, i + 3), 16));
+            i += 2;
+        }
+        else {
+            utf8.push(encoded.charCodeAt(i));
+        }
+    }
+    const bytes = Uint8Array.from(utf8);
+    const words = new Array(64).fill(0);
+    const hash = [
+        0x6a09e667, 0xbb67ae85, 0x3c6ef372, 0xa54ff53a, 0x510e527f, 0x9b05688c, 0x1f83d9ab, 0x5be0cd19,
+    ];
+    const constants = [
+        0x428a2f98, 0x71374491, 0xb5c0fbcf, 0xe9b5dba5, 0x3956c25b, 0x59f111f1, 0x923f82a4, 0xab1c5ed5,
+        0xd807aa98, 0x12835b01, 0x243185be, 0x550c7dc3, 0x72be5d74, 0x80deb1fe, 0x9bdc06a7, 0xc19bf174,
+        0xe49b69c1, 0xefbe4786, 0x0fc19dc6, 0x240ca1cc, 0x2de92c6f, 0x4a7484aa, 0x5cb0a9dc, 0x76f988da,
+        0x983e5152, 0xa831c66d, 0xb00327c8, 0xbf597fc7, 0xc6e00bf3, 0xd5a79147, 0x06ca6351, 0x14292967,
+        0x27b70a85, 0x2e1b2138, 0x4d2c6dfc, 0x53380d13, 0x650a7354, 0x766a0abb, 0x81c2c92e, 0x92722c85,
+        0xa2bfe8a1, 0xa81a664b, 0xc24b8b70, 0xc76c51a3, 0xd192e819, 0xd6990624, 0xf40e3585, 0x106aa070,
+        0x19a4c116, 0x1e376c08, 0x2748774c, 0x34b0bcb5, 0x391c0cb3, 0x4ed8aa4a, 0x5b9cca4f, 0x682e6ff3,
+        0x748f82ee, 0x78a5636f, 0x84c87814, 0x8cc70208, 0x90befffa, 0xa4506ceb, 0xbef9a3f7, 0xc67178f2,
+    ];
+    const readNumber = (values, index) => {
+        const value = values[index];
+        if (value === undefined)
+            throw new Error(`SHA-256 state index ${index} is out of bounds`);
+        return value;
+    };
+    const bitLength = bytes.length * 8;
+    const paddedLength = Math.ceil((bytes.length + 9) / 64) * 64;
+    const padded = new Uint8Array(paddedLength);
+    padded.set(bytes);
+    padded[bytes.length] = 0x80;
+    const view = new DataView(padded.buffer);
+    view.setUint32(paddedLength - 4, bitLength >>> 0);
+    view.setUint32(paddedLength - 8, Math.floor(bitLength / 0x100000000));
+    for (let offset = 0; offset < padded.length; offset += 64) {
+        for (let i = 0; i < 16; i += 1)
+            words[i] = view.getUint32(offset + i * 4);
+        for (let i = 16; i < 64; i += 1) {
+            const value = readNumber(words, i - 15);
+            const smallSigma0 = ((value >>> 7) | (value << 25)) ^ ((value >>> 18) | (value << 14)) ^ (value >>> 3);
+            const previous = readNumber(words, i - 2);
+            const smallSigma1 = ((previous >>> 17) | (previous << 15)) ^ ((previous >>> 19) | (previous << 13)) ^ (previous >>> 10);
+            words[i] = (readNumber(words, i - 16) + smallSigma0 + readNumber(words, i - 7) + smallSigma1) >>> 0;
+        }
+        let a = readNumber(hash, 0);
+        let b = readNumber(hash, 1);
+        let c = readNumber(hash, 2);
+        let d = readNumber(hash, 3);
+        let e = readNumber(hash, 4);
+        let f = readNumber(hash, 5);
+        let g = readNumber(hash, 6);
+        let h = readNumber(hash, 7);
+        for (let i = 0; i < 64; i += 1) {
+            const bigSigma1 = ((e >>> 6) | (e << 26)) ^ ((e >>> 11) | (e << 21)) ^ ((e >>> 25) | (e << 7));
+            const choose = (e & f) ^ (~e & g);
+            const temp1 = (h + bigSigma1 + choose + readNumber(constants, i) + readNumber(words, i)) >>> 0;
+            const bigSigma0 = ((a >>> 2) | (a << 30)) ^ ((a >>> 13) | (a << 19)) ^ ((a >>> 22) | (a << 10));
+            const majority = (a & b) ^ (a & c) ^ (b & c);
+            const temp2 = (bigSigma0 + majority) >>> 0;
+            h = g;
+            g = f;
+            f = e;
+            e = (d + temp1) >>> 0;
+            d = c;
+            c = b;
+            b = a;
+            a = (temp1 + temp2) >>> 0;
+        }
+        hash[0] = (readNumber(hash, 0) + a) >>> 0;
+        hash[1] = (readNumber(hash, 1) + b) >>> 0;
+        hash[2] = (readNumber(hash, 2) + c) >>> 0;
+        hash[3] = (readNumber(hash, 3) + d) >>> 0;
+        hash[4] = (readNumber(hash, 4) + e) >>> 0;
+        hash[5] = (readNumber(hash, 5) + f) >>> 0;
+        hash[6] = (readNumber(hash, 6) + g) >>> 0;
+        hash[7] = (readNumber(hash, 7) + h) >>> 0;
+    }
+    return [...hash].map((value) => value.toString(16).padStart(8, "0")).join("");
+}
+export function analysisAdapterSnapshotSha256(adapter) {
+    return sha256Hex(stableContractJson({ identity: adapter.identity, contract: adapter.contract }));
+}
+export function createAnalysisContext(input) {
+    const clean = (value, label, max) => {
+        const text = value.normalize("NFKC").replace(/\s+/g, " ").trim();
+        if (!text || text.length > max)
+            throw new Error(`${label} must be a non-empty bounded string`);
+        return text;
+    };
+    const id = clean(input.id, "Analysis id", 128);
+    if (!/^[A-Za-z0-9][A-Za-z0-9._:-]*$/.test(id))
+        throw new Error("Analysis id contains unsafe characters");
+    return {
+        version: ANALYSIS_CONTRACT_VERSION,
+        id,
+        question: clean(input.question, "Analysis question", 512),
+        assay: clean(input.assay, "Assay", 128),
+        mode: input.mode,
+        adapter: input.adapter,
+    };
+}
 //# sourceMappingURL=index.js.map

package/node_modules/@gyoungwe/plugin-api/dist/index.js.map

@@ -1 +1 @@
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