new Promise((resolve) => setTimeout(resolve, ms));
-export async function submitForExtraction(file_id, extractor_name, statementType, clientInfo){
+export async function submitForExtraction(file_id, extractor_name, statementType, clientInfo, user = null){
// submits file for extraction and returns true if extraction is successful, else returns false
+ // user parameter contains the username from redux store
let body = {}
if (extractor_name === config.rct_extractor){
- body = {"extractor": extractor_name, "parameters": {"statement": statementType}};
+ body = {"extractor": extractor_name, "parameters": {"statement": statementType, "user": user}};
}
else{
body = {"extractor": extractor_name};
diff --git a/src/utils/pdf_pipeline.js b/src/utils/pdf_pipeline.js
index 1994a88..966d177 100644
--- a/src/utils/pdf_pipeline.js
+++ b/src/utils/pdf_pipeline.js
@@ -4,9 +4,10 @@ import {submitForExtraction} from "../utils/file";
import {csvPipeline} from "../utils/csv_pipeline";
import {SET_EXTRACTION_STATUS, setExtractionStatus} from "../actions/file";
import {updateDatasetStatus} from "../actions/dataset";
+import {rctdbClient} from "./rctdb-client";
// pdf_pipeline function
-export async function pdfPipeline(file_json, dataset_json, config, clientInfo, dispatch) {
+export async function pdfPipeline(file_json, dataset_json, config, clientInfo, dispatch, user = null) {
const fileid = file_json.id;
const filename = file_json.filename;
@@ -20,7 +21,7 @@ export async function pdfPipeline(file_json, dataset_json, config, clientInfo, d
dispatch(setExtractionStatus("Extracting sentences and metadata from file"));
dispatch(updateDatasetStatus(datasetid, "in progress"));
- const pdf_extraction_submission = await submitForExtraction(fileid, pdf_extractor, statementType, clientInfo);
+ const pdf_extraction_submission = await submitForExtraction(fileid, pdf_extractor, statementType, clientInfo, user);
if (pdf_extraction_submission) {
const pdf_extraction_metadata = await getDatasetMetadataLoop(datasetid, pdf_extractor, clientInfo);
if (pdf_extraction_metadata !== null && pdf_extraction_metadata !== undefined){
@@ -40,7 +41,9 @@ export async function pdfPipeline(file_json, dataset_json, config, clientInfo, d
if (extracted_csv_file !== null && typeof extracted_csv_file.id === "string") {
console.log("Extracted csv file found after pdf extraction", extracted_csv_file);
- const csv_pipeline_status = await csvPipeline(extracted_csv_file, dataset_json, config, clientInfo, dispatch)
+ const publicationData = {datasetid: datasetid, extractedcsvfileid: extracted_csv_file.id};
+ await rctdbClient.upsertPublication(publicationData);
+ const csv_pipeline_status = await csvPipeline(extracted_csv_file, dataset_json, config, clientInfo, dispatch, user)
if (csv_pipeline_status) {
dispatch(updateDatasetStatus(datasetid, "csv-completed"));
} else {
diff --git a/src/utils/rctdb-client-example.js b/src/utils/rctdb-client-example.js
new file mode 100644
index 0000000..3ec201e
--- /dev/null
+++ b/src/utils/rctdb-client-example.js
@@ -0,0 +1,349 @@
+/**
+ * RCTDB Client Usage Examples
+ *
+ * This file demonstrates how to use the RCTDB client to interact with the RCTDB API.
+ * Make sure to install axios first: npm install axios
+ */
+import React from 'react';
+import { rctdbClient, rctdbAPI, createRCTDBClient } from './rctdb-client.js';
+
+// ============ BASIC USAGE EXAMPLES ============
+
+/**
+ * Example 1: Using the default client instance
+ */
+export async function exampleBasicUsage() {
+ try {
+ // Test connection
+ const isHealthy = await rctdbClient.testConnection();
+ console.log('RCTDB Connection:', isHealthy ? 'OK' : 'Failed');
+
+ // Get all users
+ const users = await rctdbClient.getAllUsers();
+ console.log('Users:', users);
+
+ // Get all publications
+ const publications = await rctdbClient.getAllPublications();
+ console.log('Publications:', publications);
+
+ } catch (error) {
+ console.error('Error in basic usage:', error);
+ }
+}
+
+/**
+ * Example 2: Using the convenience API
+ */
+export async function exampleConvenienceAPI() {
+ try {
+ // Using shorthand methods
+ const users = await rctdbAPI.users.getAll();
+ const publications = await rctdbAPI.publications.getAll();
+ const healthStatus = await rctdbAPI.health.check();
+
+ console.log('Users:', users.length);
+ console.log('Publications:', publications.length);
+ console.log('Health:', healthStatus);
+
+ } catch (error) {
+ console.error('Error in convenience API:', error);
+ }
+}
+
+/**
+ * Example 3: Creating a custom client with configuration
+ */
+export async function exampleCustomClient() {
+ try {
+ // Create client with custom configuration
+ const customClient = createRCTDBClient({
+ baseURL: 'http://localhost:3001/rctdb',
+ timeout: 15000,
+ headers: {
+ 'X-Custom-Header': 'MyApp/1.0'
+ }
+ });
+
+ // Set auth token if needed
+ customClient.setAuthToken('your-jwt-token-here');
+
+ const users = await customClient.getAllUsers();
+ console.log('Custom client users:', users);
+
+ } catch (error) {
+ console.error('Error in custom client:', error);
+ }
+}
+
+// ============ CRUD OPERATION EXAMPLES ============
+
+/**
+ * Example 4: User management operations
+ */
+export async function exampleUserOperations() {
+ try {
+ // Create a new user
+ const newUser = await rctdbClient.createUser({
+ name: 'John Doe',
+ email: 'john.doe@example.com',
+ role: 'researcher'
+ });
+ console.log('Created user:', newUser);
+
+ // Get user by UUID
+ const user = await rctdbClient.getUserByUuid(newUser.uuid);
+ console.log('Retrieved user:', user);
+
+ // Get all users
+ const allUsers = await rctdbClient.getAllUsers();
+ console.log('Total users:', allUsers.length);
+
+ } catch (error) {
+ console.error('Error in user operations:', error);
+ }
+}
+
+/**
+ * Example 5: Publication management operations
+ */
+export async function examplePublicationOperations() {
+ try {
+ // Create a new publication
+ const newPublication = await rctdbClient.createPublication({
+ title: 'My Research Paper',
+ abstract: 'This is an abstract of my research paper.',
+ authors: ['John Doe', 'Jane Smith'],
+ journal: 'Nature',
+ year: 2024,
+ doi: '10.1000/example.doi',
+ user_uuid: 1 // Assuming user with UUID 1 exists
+ });
+ console.log('Created publication:', newPublication);
+
+ // Get publication by UUID
+ const publication = await rctdbClient.getPublicationByUuid(newPublication.uuid);
+ console.log('Retrieved publication:', publication);
+
+ // Get annotations for this publication
+ const annotations = await rctdbClient.getPublicationAnnotations(newPublication.uuid);
+ console.log('Publication annotations:', annotations);
+
+ } catch (error) {
+ console.error('Error in publication operations:', error);
+ }
+}
+
+/**
+ * Example 6: Annotation and feedback operations
+ */
+export async function exampleAnnotationOperations() {
+ try {
+ // Create an annotation
+ const newAnnotation = await rctdbClient.createAnnotation({
+ publication_uuid: 1, // Assuming publication with UUID 1 exists
+ user_uuid: 1, // Assuming user with UUID 1 exists
+ text: 'This is an important finding',
+ page_number: 5,
+ coordinates: { x: 100, y: 200, width: 300, height: 50 },
+ annotation_type: 'highlight'
+ });
+ console.log('Created annotation:', newAnnotation);
+
+ // Update the annotation
+ const updatedAnnotation = await rctdbClient.updateAnnotation(newAnnotation.uuid, {
+ text: 'This is a very important finding - updated'
+ });
+ console.log('Updated annotation:', updatedAnnotation);
+
+ // Create feedback for the annotation
+ const feedback = await rctdbClient.createFeedback({
+ annotation_uuid: newAnnotation.uuid,
+ user_uuid: 2, // Different user providing feedback
+ feedback_type: 'agree',
+ comment: 'I agree with this annotation'
+ });
+ console.log('Created feedback:', feedback);
+
+ // Get all feedback for the annotation
+ const allFeedback = await rctdbClient.getAnnotationFeedback(newAnnotation.uuid);
+ console.log('All feedback:', allFeedback);
+
+ } catch (error) {
+ console.error('Error in annotation operations:', error);
+ }
+}
+
+// ============ ERROR HANDLING EXAMPLES ============
+
+/**
+ * Example 7: Error handling and retry logic
+ */
+export async function exampleErrorHandling() {
+ try {
+ // Try to get a non-existent user
+ const user = await rctdbClient.getUserByUuid(99999);
+ console.log('User:', user);
+ } catch (error) {
+ if (error.message.includes('not found')) {
+ console.log('User not found - this is expected');
+ } else {
+ console.error('Unexpected error:', error);
+ }
+ }
+
+ // Example with retry logic
+ const maxRetries = 3;
+ let retries = 0;
+
+ while (retries < maxRetries) {
+ try {
+ const health = await rctdbClient.checkHealth();
+ console.log('Health check successful:', health);
+ break;
+ } catch (error) {
+ retries++;
+ console.log(`Health check failed, retry ${retries}/${maxRetries}`);
+
+ if (retries >= maxRetries) {
+ console.error('Max retries reached, service unavailable');
+ throw error;
+ }
+
+ // Wait before retrying
+ await new Promise(resolve => setTimeout(resolve, 1000));
+ }
+ }
+}
+
+// ============ REACT HOOK EXAMPLES ============
+
+/**
+ * Example 8: React hook for RCTDB operations
+ */
+export function useRCTDB() {
+ const [loading, setLoading] = React.useState(false);
+ const [error, setError] = React.useState(null);
+
+ const executeWithErrorHandling = async (operation) => {
+ setLoading(true);
+ setError(null);
+
+ try {
+ const result = await operation();
+ return result;
+ } catch (err) {
+ setError(err.message);
+ throw err;
+ } finally {
+ setLoading(false);
+ }
+ };
+
+ return {
+ loading,
+ error,
+ // User operations
+ getUsers: () => executeWithErrorHandling(() => rctdbAPI.users.getAll()),
+ createUser: (data) => executeWithErrorHandling(() => rctdbAPI.users.create(data)),
+
+ // Publication operations
+ getPublications: () => executeWithErrorHandling(() => rctdbAPI.publications.getAll()),
+ createPublication: (data) => executeWithErrorHandling(() => rctdbAPI.publications.create(data)),
+
+ // Health check
+ checkHealth: () => executeWithErrorHandling(() => rctdbAPI.health.check())
+ };
+}
+
+// ============ INTEGRATION EXAMPLES ============
+
+/**
+ * Example 9: Full workflow example
+ */
+export async function exampleFullWorkflow() {
+ try {
+ console.log('Starting full workflow example...');
+
+ // 1. Check service health
+ const isHealthy = await rctdbClient.testConnection();
+ if (!isHealthy) {
+ throw new Error('RCTDB service is not available');
+ }
+
+ // 2. Create a user
+ const user = await rctdbClient.createUser({
+ name: 'Dr. Alice Research',
+ email: 'alice@university.edu',
+ role: 'principal_investigator'
+ });
+
+ // 3. Create a publication
+ const publication = await rctdbClient.createPublication({
+ title: 'Advanced Machine Learning Techniques',
+ abstract: 'A comprehensive study of modern ML approaches.',
+ authors: ['Dr. Alice Research'],
+ user_uuid: user.uuid
+ });
+
+ // 4. Create annotations
+ const annotation1 = await rctdbClient.createAnnotation({
+ publication_uuid: publication.uuid,
+ user_uuid: user.uuid,
+ text: 'Key methodology section',
+ page_number: 3,
+ annotation_type: 'note'
+ });
+
+ const annotation2 = await rctdbClient.createAnnotation({
+ publication_uuid: publication.uuid,
+ user_uuid: user.uuid,
+ text: 'Important results',
+ page_number: 7,
+ annotation_type: 'highlight'
+ });
+
+ // 5. Get all annotations for the publication
+ const allAnnotations = await rctdbClient.getPublicationAnnotations(publication.uuid);
+
+ console.log('Workflow completed successfully!');
+ console.log('Created:', {
+ user: user.uuid,
+ publication: publication.uuid,
+ annotations: allAnnotations.length
+ });
+
+ } catch (error) {
+ console.error('Workflow failed:', error);
+ }
+}
+
+// ============ EXPORT ALL EXAMPLES ============
+
+export const examples = {
+ basicUsage: exampleBasicUsage,
+ convenienceAPI: exampleConvenienceAPI,
+ customClient: exampleCustomClient,
+ userOperations: exampleUserOperations,
+ publicationOperations: examplePublicationOperations,
+ annotationOperations: exampleAnnotationOperations,
+ errorHandling: exampleErrorHandling,
+ fullWorkflow: exampleFullWorkflow
+};
+
+// Run all examples (uncomment to test)
+export async function runAllExamples() {
+ console.log('Running RCTDB Client Examples...');
+
+ for (const [name, example] of Object.entries(examples)) {
+ console.log(`\n--- ${name} ---`);
+ try {
+ await example();
+ } catch (error) {
+ console.error(`Example ${name} failed:`, error);
+ }
+ break;
+ }
+}
+
+// Auto-run the examples when this file is executed directly
+runAllExamples().catch(console.error);
\ No newline at end of file
diff --git a/src/utils/rctdb-client.js b/src/utils/rctdb-client.js
new file mode 100644
index 0000000..349bb4a
--- /dev/null
+++ b/src/utils/rctdb-client.js
@@ -0,0 +1,246 @@
+import axios from 'axios';
+
+// Configuration
+const DEFAULT_BASE_URL = process.env.NODE_ENV === 'development'
+ ? 'http://localhost:3000/api/rctdb'
+ : '/api/rctdb';
+// const DEFAULT_TIMEOUT = 60000; // 60 seconds
+
+/**
+ * RCTDB API Client
+ * Provides methods to interact with all RCTDB routes
+ */
+class RCTDBClient {
+ constructor(config = {}) {
+ this.baseURL = config.baseURL || DEFAULT_BASE_URL;
+ // this.timeout = config.timeout || DEFAULT_TIMEOUT;
+
+ // Create axios instance
+ this.client = axios.create({
+ baseURL: this.baseURL,
+ // timeout: this.timeout,
+ headers: {
+ 'Content-Type': 'application/json',
+ ...config.headers
+ }
+ });
+
+ // Add request interceptor for logging
+ this.client.interceptors.request.use(
+ (config) => {
+ console.log(`[RCTDB] ${config.method?.toUpperCase()} ${config.url}`);
+ return config;
+ },
+ (error) => {
+ console.error('[RCTDB] Request error:', error);
+ return Promise.reject(error);
+ }
+ );
+
+ // Add response interceptor for error handling
+ this.client.interceptors.response.use(
+ (response) => response,
+ (error) => {
+ console.error('[RCTDB] Response error:', error);
+ if (error.response?.data?.error) {
+ throw new Error(error.response.data.error);
+ }
+ throw error;
+ }
+ );
+ }
+
+ // ============ USER METHODS ============
+
+ /**
+ * Get all users
+ * @returns {Promise
} Array of users
+ */
+ async getAllUsers() {
+ const response = await this.client.get('/users');
+ return response.data;
+ }
+
+ /**
+ * Create a new user
+ * @param {Object} userData - User data object
+ * @returns {Promise