@aurabx/jmix-js 0.1.0

package/dist/dicom/DicomProcessor.js

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+import * as fs from 'fs/promises';
+import * as path from 'path';
+import { DicomError } from '../types/index.js';
+import daikon from 'daikon';
+const DICOM_MAGIC_OFFSET = 128;
+const DICOM_MAGIC_SIGNATURE = 'DICM';
+function toArrayBuffer(buf) {
+    const ab = new ArrayBuffer(buf.byteLength);
+    const view = new Uint8Array(ab);
+    view.set(buf);
+    return ab;
+}
+export class DicomProcessor {
+    /**
+     * Process a DICOM directory and extract metadata
+     */
+    async processDicomFolder(dicomPath, config) {
+        try {
+            const dicomFiles = await this.findDicomFiles(dicomPath);
+            if (dicomFiles.length === 0) {
+                // Fallback to config data if no DICOM files found
+                return this.createMetadataFromConfig(config);
+            }
+            // Parse files with Daikon and group by series
+            const images = [];
+            const seriesMap = new Map();
+            const modalitiesSet = new Set();
+            for (const f of dicomFiles) {
+                try {
+                    const buf = await fs.readFile(f);
+                    const view = new DataView(toArrayBuffer(buf));
+                    const image = daikon.Series.parseImage(view);
+                    if (!image)
+                        continue;
+                    images.push(image);
+                    const seriesId = image.getSeriesId ? image.getSeriesId() : path.dirname(f);
+                    const arr = seriesMap.get(seriesId) || [];
+                    arr.push(image);
+                    seriesMap.set(seriesId, arr);
+                    // Try to read modality if available
+                    try {
+                        const modality = (image.getModality && image.getModality()) || this.readTag(image, 0x0008, 0x0060) || 'UNKNOWN';
+                        if (modality)
+                            modalitiesSet.add(String(modality));
+                    }
+                    catch {
+                        // ignore modality errors
+                    }
+                }
+                catch {
+                    // skip unreadable file
+                }
+            }
+            const series = [];
+            for (const [sid, imgs] of seriesMap.entries()) {
+                series.push({
+                    series_uid: String(sid),
+                    modality: 'UNKNOWN',
+                    instance_count: imgs.length,
+                });
+            }
+            // Attempt to extract some study-level tags from the first image
+            let study_description = undefined;
+            let study_uid = undefined;
+            let study_date = undefined;
+            let patient_name = config?.patient.name;
+            let patient_id = config?.patient.id;
+            let patient_dob = config?.patient.dob;
+            let patient_sex = config?.patient.sex;
+            const first = images[0];
+            if (first) {
+                study_description = this.readTag(first, 0x0008, 0x1030) || 'Study';
+                study_uid = this.readTag(first, 0x0020, 0x000D) || this.generateStudyUID();
+                const sd = this.readTag(first, 0x0008, 0x0020);
+                study_date = sd && String(sd).length === 8 ? DicomProcessor.formatDicomDate(String(sd)) : new Date().toISOString().split('T')[0];
+                patient_name = this.readTag(first, 0x0010, 0x0010) || patient_name;
+                patient_id = this.readTag(first, 0x0010, 0x0020) || patient_id;
+                const dob = this.readTag(first, 0x0010, 0x0030);
+                patient_dob = dob && String(dob).length === 8 ? DicomProcessor.formatDicomDate(String(dob)) : patient_dob;
+                patient_sex = this.readTag(first, 0x0010, 0x0040) || patient_sex;
+            }
+            const metadata = {
+                patient_name,
+                patient_id,
+                patient_dob,
+                patient_sex,
+                study_description,
+                study_uid,
+                study_date,
+                modalities: Array.from(modalitiesSet.size ? modalitiesSet : new Set(['UNKNOWN'])),
+                series_count: seriesMap.size || 1,
+                instance_count: images.length,
+                series,
+            };
+            return metadata;
+        }
+        catch (error) {
+            throw new DicomError(`Failed to process DICOM folder: ${dicomPath}`, error instanceof Error ? error : new Error(String(error)));
+        }
+    }
+    /**
+     * Recursively find DICOM files in a directory
+     */
+    async findDicomFiles(dirPath) {
+        const dicomFiles = [];
+        try {
+            const entries = await fs.readdir(dirPath, { withFileTypes: true });
+            for (const entry of entries) {
+                const fullPath = path.join(dirPath, entry.name);
+                if (entry.isDirectory()) {
+                    // Recursively search subdirectories
+                    const subDirFiles = await this.findDicomFiles(fullPath);
+                    dicomFiles.push(...subDirFiles);
+                }
+                else if (entry.isFile()) {
+                    if (await this.isDicomFile(fullPath)) {
+                        dicomFiles.push(fullPath);
+                    }
+                }
+            }
+        }
+        catch (error) {
+            throw new DicomError(`Failed to read directory: ${dirPath}`, error instanceof Error ? error : new Error(String(error)));
+        }
+        return dicomFiles;
+    }
+    /**
+     * Check if a file is a DICOM file by checking the magic signature
+     */
+    async isDicomFile(filePath) {
+        try {
+            // Check file extension first (quick check)
+            const ext = path.extname(filePath).toLowerCase();
+            if (['.dcm', '.dicom'].includes(ext)) {
+                return true;
+            }
+            // Check for DICM magic number at offset 128
+            const fileHandle = await fs.open(filePath, 'r');
+            const buffer = Buffer.alloc(4);
+            await fileHandle.read(buffer, 0, 4, DICOM_MAGIC_OFFSET);
+            await fileHandle.close();
+            return buffer.toString('ascii') === DICOM_MAGIC_SIGNATURE;
+        }
+        catch {
+            // If we can't read the file, assume it's not a DICOM file
+            return false;
+        }
+    }
+    /**
+     * Create metadata from config when DICOM parsing fails or no files found
+     */
+    createMetadataFromConfig(config) {
+        return {
+            patient_name: config?.patient.name,
+            patient_id: config?.patient.id,
+            patient_dob: config?.patient.dob,
+            patient_sex: config?.patient.sex,
+            study_description: 'Study from configuration',
+            study_uid: this.generateStudyUID(),
+            study_date: new Date().toISOString().split('T')[0],
+            modalities: ['UNKNOWN'],
+            series_count: 1,
+            instance_count: 0,
+            series: [],
+        };
+    }
+    /**
+     * Generate a study UID (placeholder implementation)
+     */
+    generateStudyUID() {
+        // Simple UID generation - in production would use proper DICOM UID format
+        const timestamp = Date.now();
+        const random = Math.floor(Math.random() * 10000);
+        return `1.2.3.${timestamp}.${random}`;
+    }
+    /**
+     * Estimate series count based on file naming patterns or directory structure
+     */
+    estimateSeriesCount(files) {
+        // Simple estimation based on directory structure
+        const directories = new Set();
+        for (const file of files) {
+            directories.add(path.dirname(file));
+        }
+        return Math.max(1, directories.size);
+    }
+    /**
+     * Attempt to read a DICOM tag value using Daikon's API (best-effort)
+     */
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    readTag(image, group, element) {
+        try {
+            if (image && image.getTag && typeof image.getTag === 'function') {
+                const tag = image.getTag(group, element);
+                if (tag && tag.value && tag.value.length) {
+                    return String(tag.value[0]);
+                }
+            }
+        }
+        catch {
+            // ignore
+        }
+        return undefined;
+    }
+    /**
+     * Format DICOM date to ISO format
+     */
+    static formatDicomDate(dicomDate) {
+        if (!dicomDate || dicomDate.length !== 8) {
+            return new Date().toISOString().split('T')[0];
+        }
+        const year = dicomDate.substring(0, 4);
+        const month = dicomDate.substring(4, 6);
+        const day = dicomDate.substring(6, 8);
+        return `${year}-${month}-${day}`;
+    }
+    /**
+     * Format DICOM person name to readable format
+     */
+    static formatDicomPersonName(dicomName) {
+        if (!dicomName)
+            return '';
+        // DICOM names are in format: "Last^First^Middle^Prefix^Suffix"
+        const parts = dicomName.split('^');
+        const last = parts[0] || '';
+        const first = parts[1] || '';
+        const middle = parts[2] || '';
+        return [first, middle, last].filter(Boolean).join(' ').trim();
+    }
+}
+//# sourceMappingURL=DicomProcessor.js.map

package/dist/dicom/DicomProcessor.js.map

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package/dist/index.d.ts

@@ -0,0 +1,6 @@
+export { JmixBuilder, type JmixBuilderOptions } from './JmixBuilder.js';
+export { SchemaValidator, type SchemaValidatorOptions, } from './validation/SchemaValidator.js';
+export { DicomProcessor } from './dicom/DicomProcessor.js';
+export * from './types/index.js';
+export type { JmixEnvelope, Config, Manifest, Metadata, Audit, Files, DicomMetadata, Patient, ContactVariant, Contact, Security, Consent, Encryption, SenderAssertion, } from './types/index.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,KAAK,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AACxE,OAAO,EACL,eAAe,EACf,KAAK,sBAAsB,GAC5B,MAAM,iCAAiC,CAAC;AACzC,OAAO,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAC;AAG3D,cAAc,kBAAkB,CAAC;AAGjC,YAAY,EACV,YAAY,EACZ,MAAM,EACN,QAAQ,EACR,QAAQ,EACR,KAAK,EACL,KAAK,EACL,aAAa,EACb,OAAO,EACP,cAAc,EACd,OAAO,EACP,QAAQ,EACR,OAAO,EACP,UAAU,EACV,eAAe,GAChB,MAAM,kBAAkB,CAAC"}

package/dist/index.js

@@ -0,0 +1,8 @@
+// JMIX TypeScript Library - Main Entry Point
+// JSON Medical Interchange format for secure medical data exchange
+export { JmixBuilder } from './JmixBuilder.js';
+export { SchemaValidator, } from './validation/SchemaValidator.js';
+export { DicomProcessor } from './dicom/DicomProcessor.js';
+// Export all types
+export * from './types/index.js';
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,6CAA6C;AAC7C,mEAAmE;AAEnE,OAAO,EAAE,WAAW,EAA2B,MAAM,kBAAkB,CAAC;AACxE,OAAO,EACL,eAAe,GAEhB,MAAM,iCAAiC,CAAC;AACzC,OAAO,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAC;AAE3D,mBAAmB;AACnB,cAAc,kBAAkB,CAAC"}

package/dist/types/index.d.ts

@@ -0,0 +1,165 @@
+export interface Contact {
+    system?: string;
+    value: string;
+    use_field?: string;
+}
+export interface ContactVariant {
+    name: string;
+    id: string;
+    contact: string | Contact;
+}
+export interface PatientIdentifier {
+    system: string;
+    value: string;
+    use_field?: string;
+}
+export interface Patient {
+    name: string;
+    id: string;
+    dob?: string;
+    sex?: 'M' | 'F' | 'O' | 'U';
+    identifiers?: PatientIdentifier[];
+}
+export interface Consent {
+    status: 'granted' | 'denied' | 'pending';
+    scope?: string[];
+    method?: string;
+}
+export interface Security {
+    classification: 'public' | 'internal' | 'confidential' | 'restricted';
+    payload_hash?: string;
+}
+export interface Encryption {
+    algorithm: 'AES-256-GCM';
+    ephemeral_public_key: string;
+    iv: string;
+    auth_tag: string;
+}
+export interface SenderAssertion {
+    signing_key: {
+        alg: string;
+        public_key: string;
+        fingerprint: string;
+    };
+    key_reference?: string;
+    signed_fields: string[];
+    signature: string;
+    expires_at?: string;
+    directory_attestation?: {
+        provider: string;
+        attestation_signature: string;
+        attestation_timestamp: string;
+        attestation_public_key: string;
+    };
+}
+export interface Manifest {
+    jmix_version: string;
+    envelope_id: string;
+    created_at: string;
+    sender: ContactVariant & {
+        assertion?: SenderAssertion;
+    };
+    requester?: ContactVariant & {
+        assertion?: SenderAssertion;
+    };
+    receivers: ContactVariant[];
+    patient: Patient;
+    security: Security;
+    consent?: Consent;
+    custom_tags?: string[];
+    report?: {
+        file: string;
+    };
+    deid_keys?: string[];
+    encryption?: Encryption;
+}
+export interface DicomMetadata {
+    patient_name?: string;
+    patient_id?: string;
+    patient_dob?: string;
+    patient_sex?: string;
+    study_description?: string;
+    study_uid?: string;
+    study_date?: string;
+    modalities: string[];
+    series_count: number;
+    instance_count: number;
+    series?: Array<{
+        series_uid: string;
+        series_description?: string;
+        modality: string;
+        instance_count: number;
+    }>;
+}
+export interface Metadata {
+    patient: Patient;
+    study: {
+        description?: string;
+        uid?: string;
+        date?: string;
+    };
+    dicom: DicomMetadata;
+    custom_metadata?: Record<string, unknown>;
+}
+export interface AuditEntityRef {
+    id: string;
+    name?: string;
+}
+export interface AuditEntry {
+    event: string;
+    by: AuditEntityRef;
+    to?: AuditEntityRef;
+    timestamp: string;
+    assertion?: SenderAssertion;
+}
+export interface Audit {
+    audit: AuditEntry[];
+}
+export interface FileEntry {
+    path: string;
+    size: number;
+    hash: string;
+    mime_type?: string;
+    description?: string;
+}
+export interface Files {
+    payload_directory: string;
+    files: FileEntry[];
+    total_size: number;
+    file_count: number;
+}
+export interface JmixEnvelope {
+    manifest: Manifest;
+    metadata: Metadata;
+    audit: Audit;
+    files?: Files;
+}
+export interface Config {
+    version: string;
+    sender: ContactVariant;
+    requester?: ContactVariant;
+    receivers: ContactVariant[];
+    patient: Patient;
+    security: Security;
+    consent?: Consent;
+    custom_tags?: string[];
+    report?: {
+        file: string;
+    };
+    deid_keys?: string[];
+}
+export declare class JmixError extends Error {
+    readonly cause?: Error | undefined;
+    constructor(message: string, cause?: Error | undefined);
+}
+export declare class ValidationError extends JmixError {
+    readonly errors: string[];
+    constructor(message: string, errors?: string[]);
+}
+export declare class CryptographyError extends JmixError {
+    constructor(message: string, cause?: Error);
+}
+export declare class DicomError extends JmixError {
+    constructor(message: string, cause?: Error);
+}
+//# sourceMappingURL=index.d.ts.map

package/dist/types/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/types/index.js

@@ -0,0 +1,31 @@
+// JMIX Core Types - TypeScript interfaces for JMIX envelope components
+// Error types
+export class JmixError extends Error {
+    cause;
+    constructor(message, cause) {
+        super(message);
+        this.cause = cause;
+        this.name = 'JmixError';
+    }
+}
+export class ValidationError extends JmixError {
+    errors;
+    constructor(message, errors = []) {
+        super(message);
+        this.errors = errors;
+        this.name = 'ValidationError';
+    }
+}
+export class CryptographyError extends JmixError {
+    constructor(message, cause) {
+        super(message, cause);
+        this.name = 'CryptographyError';
+    }
+}
+export class DicomError extends JmixError {
+    constructor(message, cause) {
+        super(message, cause);
+        this.name = 'DicomError';
+    }
+}
+//# sourceMappingURL=index.js.map

package/dist/types/index.js.map

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package/dist/validation/SchemaValidator.d.ts

@@ -0,0 +1,25 @@
+export interface SchemaValidatorOptions {
+    schemaPath?: string;
+    strictMode?: boolean;
+}
+export declare class SchemaValidator {
+    private ajv;
+    private schemaPath;
+    private schemaCache;
+    constructor(options?: SchemaValidatorOptions);
+    private loadSchema;
+    private getSchemaPath;
+    validateManifest(data: unknown): Promise<void>;
+    validateMetadata(data: unknown): Promise<void>;
+    validateAudit(data: unknown): Promise<void>;
+    validateFiles(data: unknown): Promise<void>;
+    private validate;
+    validateEnvelope(envelope: {
+        manifest: unknown;
+        metadata: unknown;
+        audit: unknown;
+        files?: unknown;
+    }): Promise<void>;
+    isSchemaAvailable(schemaName?: string): Promise<boolean>;
+}
+//# sourceMappingURL=SchemaValidator.d.ts.map

package/dist/validation/SchemaValidator.d.ts.map

@@ -0,0 +1 @@
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package/dist/validation/SchemaValidator.js

@@ -0,0 +1,125 @@
+import Ajv from 'ajv';
+import addFormats from 'ajv-formats';
+import * as fs from 'fs/promises';
+import * as path from 'path';
+import { ValidationError } from '../types/index.js';
+export class SchemaValidator {
+    ajv;
+    schemaPath;
+    schemaCache = new Map();
+    constructor(options = {}) {
+        this.schemaPath =
+            options.schemaPath ||
+                process.env.JMIX_SCHEMA_PATH ||
+                path.resolve(process.cwd(), '../jmix/schemas');
+        this.ajv = new Ajv({
+            allErrors: true,
+            strict: options.strictMode ?? true,
+            loadSchema: this.loadSchema.bind(this),
+        });
+        addFormats(this.ajv);
+    }
+    async loadSchema(uri) {
+        if (this.schemaCache.has(uri)) {
+            return this.schemaCache.get(uri);
+        }
+        try {
+            const schemaContent = await fs.readFile(uri, 'utf-8');
+            const schema = JSON.parse(schemaContent);
+            this.schemaCache.set(uri, schema);
+            return schema;
+        }
+        catch (error) {
+            throw new ValidationError(`Failed to load schema from ${uri}`, [
+                error instanceof Error ? error.message : String(error),
+            ]);
+        }
+    }
+    getSchemaPath(schemaName) {
+        return path.join(this.schemaPath, `${schemaName}.schema.json`);
+    }
+    async validateManifest(data) {
+        await this.validate('manifest', data);
+    }
+    async validateMetadata(data) {
+        await this.validate('metadata', data);
+    }
+    async validateAudit(data) {
+        await this.validate('audit', data);
+    }
+    async validateFiles(data) {
+        await this.validate('files', data);
+    }
+    async validate(schemaName, data) {
+        const schemaPath = this.getSchemaPath(schemaName);
+        try {
+            // Check if schema file exists
+            await fs.access(schemaPath);
+        }
+        catch {
+            // Schema file doesn't exist, skip validation gracefully
+            console.warn(`Schema validation skipped: ${schemaPath} not found`);
+            return;
+        }
+        try {
+            const schema = await this.loadSchema(schemaPath);
+            const validate = this.ajv.compile(schema);
+            const valid = validate(data);
+            if (!valid) {
+                const errors = validate.errors?.map((error) => {
+                    const instancePath = error.instancePath || 'root';
+                    return `${instancePath}: ${error.message}`;
+                }) || [];
+                throw new ValidationError(`${schemaName} validation failed`, errors);
+            }
+        }
+        catch (error) {
+            if (error instanceof ValidationError &&
+                error.message.includes('validation failed')) {
+                throw error;
+            }
+            // For schema loading errors, just skip validation gracefully
+            console.warn(`Schema validation error for ${schemaName}, skipping: ${error instanceof Error ? error.message : String(error)}`);
+            return;
+        }
+    }
+    async validateEnvelope(envelope) {
+        const validationPromises = [
+            this.validateManifest(envelope.manifest),
+            this.validateMetadata(envelope.metadata),
+            this.validateAudit(envelope.audit),
+        ];
+        if (envelope.files) {
+            validationPromises.push(this.validateFiles(envelope.files));
+        }
+        try {
+            await Promise.all(validationPromises);
+        }
+        catch (error) {
+            if (error instanceof ValidationError) {
+                throw error;
+            }
+            throw new ValidationError('Envelope validation failed', [
+                error instanceof Error ? error.message : String(error),
+            ]);
+        }
+    }
+    // Check if schema files are available
+    async isSchemaAvailable(schemaName) {
+        if (schemaName) {
+            try {
+                await fs.access(this.getSchemaPath(schemaName));
+                return true;
+            }
+            catch {
+                return false;
+            }
+        }
+        // Check if any schema files are available
+        const schemaNames = ['manifest', 'metadata', 'audit', 'files'];
+        const checks = schemaNames.map((name) => this.isSchemaAvailable(name));
+        const results = await Promise.all(checks);
+        return results.some((available) => available);
+    }
+}
+//# sourceMappingURL=SchemaValidator.js.map

package/dist/validation/SchemaValidator.js.map

@@ -0,0 +1 @@
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package/jest.config.json

@@ -0,0 +1,20 @@
+{
+  "preset": "ts-jest/presets/default-esm",
+  "extensionsToTreatAsEsm": [".ts"],
+  "moduleNameMapper": {
+    "^(\\.{1,2}/.*)\\.js$": "$1"
+  },
+  "testEnvironment": "node",
+  "testMatch": ["**/tests/**/*.test.ts", "**/__tests__/**/*.test.ts"],
+  "collectCoverageFrom": ["src/**/*.ts", "!src/**/*.d.ts", "!src/**/*.test.ts"],
+  "coverageDirectory": "coverage",
+  "coverageReporters": ["text", "lcov", "html"],
+  "transform": {
+    "^.+\\.ts$": [
+      "ts-jest",
+      {
+        "useESM": true
+      }
+    ]
+  }
+}