@bio-rs/biors-wasm 0.51.0 → 0.53.0

package/README.md

@@ -6,9 +6,13 @@ WebAssembly/JavaScript bindings for [bio-rs](https://github.com/bio-rs/bio-rs) c
 
 ```javascript
 import {
+  browserExecutionPolicy,
+  inspectBrowserFile,
+  validateBrowserFile,
   parseFasta,
   validateFasta,
   tokenize,
+  tokenizeBrowserFile,
   buildModelInputWithPolicy,
   runWorkflow,
 } from "@bio-rs/biors-wasm";
@@ -33,8 +37,24 @@ const dnaWorkflow = runWorkflow({
   profile: "dna-iupac",
   maxLength: 8,
 });
+
+const policy = browserExecutionPolicy();
+const fileInput = {
+  name: "protein.fasta",
+  format: "fasta",
+  bytes,
+  kind: "protein",
+  profile: "protein-20",
+};
+const inspected = inspectBrowserFile(fileInput);
+const browserValidation = validateBrowserFile(fileInput);
+const browserTokens = tokenizeBrowserFile(fileInput);
 ```
 
+The browser helpers are local-first by contract: they accept caller-owned
+`Uint8Array` input, enforce the documented size policy, do not call `fetch`, do
+not upload input data, and do not persist records.
+
 ## Development
 
 ```bash

package/biors_wasm.d.ts

@@ -155,12 +155,85 @@ export interface WorkflowOutput {
 
 
 
+export type BrowserBioFormat = "fasta" | "fastq" | "pdb" | "smiles";
+
+export interface BrowserFileInput {
+    bytes: Uint8Array;
+    name?: string;
+    format?: BrowserBioFormat;
+    kind?: "auto" | "protein" | "dna" | "rna";
+    profile?: "protein-20" | "protein-20-special" | "dna-iupac" | "dna-iupac-special" | "rna-iupac" | "rna-iupac-special";
+}
+
+export interface BrowserExecutionPolicy {
+    schema_version: "biors.browser_tooling.v0";
+    execution_mode: "wasm_local";
+    network_access: "none";
+    uploads_input_data: false;
+    external_model_calls: false;
+    persistence: "caller_controlled";
+    max_input_bytes: number;
+    warning_input_bytes: number;
+    streaming: {
+        supported: false;
+        behavior: string;
+        caller_guidance: string;
+    };
+    supported_validation_formats: BrowserBioFormat[];
+    supported_tokenization_formats: "fasta"[];
+}
+
+export interface BrowserFileDescriptor {
+    name?: string;
+    format: BrowserBioFormat;
+    size_bytes: number;
+    content_sha256: string;
+    input_hash?: string;
+}
+
+export interface BrowserFileWarning {
+    code: string;
+    message: string;
+}
+
+export interface BrowserFileInspection {
+    schema_version: "biors.browser_tooling.v0";
+    file: BrowserFileDescriptor;
+    accepted: boolean;
+    warnings: BrowserFileWarning[];
+}
+
+export interface BrowserValidationOutput {
+    schema_version: "biors.browser_tooling.v0";
+    file: BrowserFileDescriptor;
+    report: unknown;
+    warnings: BrowserFileWarning[];
+}
+
+export interface BrowserTokenizationOutput {
+    schema_version: "biors.browser_tooling.v0";
+    file: BrowserFileDescriptor;
+    tokenization: TokenizeOutput;
+    model_input_policy_hint: {
+        max_length_required: boolean;
+        supported_padding: Array<"fixed_length" | "no_padding">;
+        note: string;
+    };
+    warnings: BrowserFileWarning[];
+}
+
+
+
+export function browserExecutionPolicy(): any;
+
 export function buildModelInput(tokenized: any, max_length: number): any;
 
 export function buildModelInputWithPolicy(tokenized: any, max_length: number, pad_token_id: number, padding: string): any;
 
 export function init_panic_hook(): void;
 
+export function inspectBrowserFile(input: any): any;
+
 /**
  * Parse FASTA bytes into an array of sequence records.
  */
@@ -170,6 +243,10 @@ export function runWorkflow(config: any): any;
 
 export function tokenize(records: any, profile: string): any;
 
+export function tokenizeBrowserFile(input: any): any;
+
+export function validateBrowserFile(input: any): any;
+
 /**
  * Validate FASTA bytes and return a structured validation report.
  */

package/biors_wasm.js

@@ -5,5 +5,5 @@ import { __wbg_set_wasm } from "./biors_wasm_bg.js";
 __wbg_set_wasm(wasm);
 wasm.__wbindgen_start();
 export {
-    buildModelInput, buildModelInputWithPolicy, init_panic_hook, parseFasta, runWorkflow, tokenize, validateFasta
+    browserExecutionPolicy, buildModelInput, buildModelInputWithPolicy, init_panic_hook, inspectBrowserFile, parseFasta, runWorkflow, tokenize, tokenizeBrowserFile, validateBrowserFile, validateFasta
 } from "./biors_wasm_bg.js";

package/biors_wasm_bg.js

@@ -1,3 +1,14 @@
+/**
+ * @returns {any}
+ */
+export function browserExecutionPolicy() {
+    const ret = wasm.browserExecutionPolicy();
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return takeFromExternrefTable0(ret[0]);
+}
+
 /**
  * @param {any} tokenized
  * @param {number} max_length
@@ -32,6 +43,18 @@ export function init_panic_hook() {
     wasm.init_panic_hook();
 }
 
+/**
+ * @param {any} input
+ * @returns {any}
+ */
+export function inspectBrowserFile(input) {
+    const ret = wasm.inspectBrowserFile(input);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return takeFromExternrefTable0(ret[0]);
+}
+
 /**
  * Parse FASTA bytes into an array of sequence records.
  * @param {Uint8Array} bytes
@@ -74,6 +97,30 @@ export function tokenize(records, profile) {
     return takeFromExternrefTable0(ret[0]);
 }
 
+/**
+ * @param {any} input
+ * @returns {any}
+ */
+export function tokenizeBrowserFile(input) {
+    const ret = wasm.tokenizeBrowserFile(input);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return takeFromExternrefTable0(ret[0]);
+}
+
+/**
+ * @param {any} input
+ * @returns {any}
+ */
+export function validateBrowserFile(input) {
+    const ret = wasm.validateBrowserFile(input);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return takeFromExternrefTable0(ret[0]);
+}
+
 /**
  * Validate FASTA bytes and return a structured validation report.
  * @param {Uint8Array} bytes
@@ -91,6 +138,10 @@ export function validateFasta(bytes, kind) {
     }
     return takeFromExternrefTable0(ret[0]);
 }
+export function __wbg___wbindgen_is_null_52ff4ec04186736f(arg0) {
+    const ret = arg0 === null;
+    return ret;
+}
 export function __wbg___wbindgen_is_undefined_29a43b4d42920abd(arg0) {
     const ret = arg0 === undefined;
     return ret;

package/biors_wasm_bg.wasm.d.ts

@@ -1,13 +1,17 @@
 /* tslint:disable */
 /* eslint-disable */
 export const memory: WebAssembly.Memory;
-export const runWorkflow: (a: any) => [number, number, number];
-export const buildModelInput: (a: any, b: number) => [number, number, number];
-export const buildModelInputWithPolicy: (a: any, b: number, c: number, d: number, e: number) => [number, number, number];
-export const init_panic_hook: () => void;
+export const browserExecutionPolicy: () => [number, number, number];
+export const inspectBrowserFile: (a: any) => [number, number, number];
+export const validateBrowserFile: (a: any) => [number, number, number];
+export const tokenizeBrowserFile: (a: any) => [number, number, number];
 export const parseFasta: (a: number, b: number) => [number, number, number];
 export const validateFasta: (a: number, b: number, c: number, d: number) => [number, number, number];
+export const buildModelInput: (a: any, b: number) => [number, number, number];
+export const buildModelInputWithPolicy: (a: any, b: number, c: number, d: number, e: number) => [number, number, number];
 export const tokenize: (a: any, b: number, c: number) => [number, number, number];
+export const runWorkflow: (a: any) => [number, number, number];
+export const init_panic_hook: () => void;
 export const __wbindgen_malloc: (a: number, b: number) => number;
 export const __wbindgen_realloc: (a: number, b: number, c: number, d: number) => number;
 export const __wbindgen_exn_store: (a: number) => void;

package/index.d.ts

@@ -3,9 +3,13 @@
 // Re-exports and refines the auto-generated wasm-pack types.
 
 export {
+    browserExecutionPolicy,
+    inspectBrowserFile,
     parseFasta,
+    validateBrowserFile,
     validateFasta,
     tokenize,
+    tokenizeBrowserFile,
     buildModelInput,
     buildModelInputWithPolicy,
     runWorkflow,
@@ -25,13 +29,25 @@ export type {
     WorkflowConfig,
     WorkflowReadinessIssue,
     WorkflowOutput,
+    BrowserBioFormat,
+    BrowserFileInput,
+    BrowserExecutionPolicy,
+    BrowserFileDescriptor,
+    BrowserFileWarning,
+    BrowserFileInspection,
+    BrowserValidationOutput,
+    BrowserTokenizationOutput,
 } from "./biors_wasm.d.ts";
 
 // Refine function signatures for consumers
 declare module "./biors_wasm.js" {
+    export function browserExecutionPolicy(): BrowserExecutionPolicy;
+    export function inspectBrowserFile(input: BrowserFileInput): BrowserFileInspection;
+    export function validateBrowserFile(input: BrowserFileInput): BrowserValidationOutput;
     export function parseFasta(bytes: Uint8Array): FastaRecord[];
     export function validateFasta(bytes: Uint8Array, kind: string): ValidationReport;
     export function tokenize(records: FastaRecord[], profile: string): TokenizeOutput;
+    export function tokenizeBrowserFile(input: BrowserFileInput): BrowserTokenizationOutput;
     export function buildModelInput(tokenized: TokenizedRecord[], maxLength: number): ModelInputOutput;
     export function buildModelInputWithPolicy(
         tokenized: TokenizedRecord[],

package/package.json

@@ -2,7 +2,7 @@
   "name": "@bio-rs/biors-wasm",
   "type": "module",
   "description": "WebAssembly bindings for bio-rs biological sequence processing",
-  "version": "0.51.0",
+  "version": "0.53.0",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",