Use setExtractionStatus action/reducer to propagate the message in th…

package.json

@@ -1,6 +1,6 @@
 {
 	"name": "consort-frontend",
-	"version": "0.8.0",
+	"version": "0.9.0",
 	"description": "",
 	"engines": {
 		"npm": ">=8.11",

src/actions/client.js

@@ -16,15 +16,6 @@ import {ADD_FILE_TO_DATASET, addFileToDataset, CREATE_DATASETS, createDataset} f
 
 const clientInfo = await getClientInfo();
 
-export function setStatement(statementType) {
-	return (dispatch) => {
-		dispatch({
-			type: 'SET_STATEMENT_TYPE',
-			statementType: statementType,
-			receivedAt: Date.now(),
-		});
-	};
-}
 
 // createUploadExtract thunk function
 export function createUploadExtract(file, config) {
@@ -43,29 +34,30 @@ export function createUploadExtract(file, config) {
 			if (file_json !== undefined){
 				file_json["filename"] = file.name;
 				// submit uploaded file for extraction
+				dispatch(setExtractionStatus("Analyzing file"));
 				if (file.type == "application/vnd.openxmlformats-officedocument.wordprocessingml.document" || file.type =="application/msword"){
 					const word_pipeline_status = await wordPipeline(file_json, dataset_json, config, clientInfo);
 					if (word_pipeline_status) {
-						console.log("File extraction complete.");
-						dispatch(setExtractionStatus(SET_EXTRACTION_STATUS, true));
+						console.log("File extraction complete");
+						dispatch(setExtractionStatus("File extraction complete"));
 
 					}
 					else {
 						console.error("File extraction failed");
-						dispatch(setExtractionStatus(SET_EXTRACTION_STATUS, false));
+						dispatch(setExtractionStatus("File extraction failed"));
 					}
-					
+
 				}
 				else if (file.type == "application/pdf") {
 					const pdf_pipeline_status = await pdfPipeline(file_json, dataset_json, config, clientInfo);
 					if (pdf_pipeline_status) {
 						console.log("File extraction complete.");
-						dispatch(setExtractionStatus(SET_EXTRACTION_STATUS, true));
+						dispatch(setExtractionStatus("File extraction complete"));
 
 					}
 					else {
 						console.error("File extraction failed");
-						dispatch(setExtractionStatus(SET_EXTRACTION_STATUS, false));
+						dispatch(setExtractionStatus("File extraction failed"));
 					}
 
 					// TODO add extracted output files to dataset state
@@ -75,20 +67,20 @@ export function createUploadExtract(file, config) {
 				else {
 					// TODO add error action
 					console.error("Error in file type");
-					dispatch(setExtractionStatus(SET_EXTRACTION_STATUS, false));
+					dispatch(setExtractionStatus("Error in file type"));
 				}
 				// after submitting uploaded file for extraction, add the file to dataset state
 				dispatch(addFileToDataset(ADD_FILE_TO_DATASET, file_json));
 			}
 			else {
 				console.error("Error in clowder upload of file ", file.name)
-				dispatch(setExtractionStatus(SET_EXTRACTION_STATUS, false));
+				dispatch(setExtractionStatus("Error in clowder upload of file " + file.name));
 			}
 		}
 		else {
 			console.error("Error in dataset creation");
-			dispatch(setExtractionStatus(SET_EXTRACTION_STATUS, false));
-		}	
+			dispatch(setExtractionStatus("Error in dataset creation"));
+		}
 	};
 }
 

src/actions/file.js

@@ -89,10 +89,10 @@ export function fetchFileMetadataJsonld(id) {
 }
 
 export const SET_EXTRACTION_STATUS = "SET_EXTRACTION_STATUS";
-export function setExtractionStatus(type, status) {
+export function setExtractionStatus(status) {
 	return (dispatch) => {
 		dispatch({
-			type: type,
+			type: SET_EXTRACTION_STATUS,
 			extractionStatus: status
 		});
 	};

src/components/childComponents/CreateAndUpload.js

@@ -13,7 +13,7 @@ import {getClientInfo} from "../../utils/common";
 import Dropfile from "./Dropfile";
 import {createUploadExtract} from "../../actions/client";
 import {getDatasetMetadata, getFileInDataset} from "../../utils/dataset";
-import {fetchFilePreviews} from "../../actions/file";
+import { fetchFilePreviews, SET_EXTRACTION_STATUS, setExtractionStatus } from "../../actions/file";
 import {SET_DATASET_METADATA, setDatasetMetadata} from "../../actions/dataset";
 import {SET_STATEMENT_TYPE, setStatement} from '../../actions/statement';
 import config from "../../app.config";
@@ -27,7 +27,6 @@ export default function CreateAndUpload() {
 	const rctExtractor = config.rct_extractor;
 
 	const [mouseHover, setMouseHover] = useState(false); // mouse hover state for dropzone
-	const [statementTypeSelected, setStatementTypeSelected] = useState(false); // user choice of statement type consort or spirit
 	const [loading, setLoading] = useState(false); // loading overlay state and button disabled state. set to active when dropfile is active
 	const [loading_text, setLoadingText] = useState("Processing"); // loading overlay text.
 	const [filename, setFilename] = useState(''); // uploaded filename
@@ -39,11 +38,11 @@ export default function CreateAndUpload() {
 	const extractionStatus = useSelector(state => state.file.extractionStatus);
 	const listFilePreviews = (fileId, clientInfo) => dispatch(fetchFilePreviews(fileId, clientInfo));
 	const datasetMetadata = (json) => dispatch(setDatasetMetadata(SET_DATASET_METADATA, json));
+	const statementType = useSelector(state => state.statement.statementType); 
 
 	const handleStatementChange = (event) => {
 		dispatch(setStatement(SET_STATEMENT_TYPE, event.target.value));
 		config.statementType = event.target.value;
-		setStatementTypeSelected(true);
 	};
 
 	const onDropFile = (file) => {
@@ -55,13 +54,13 @@ export default function CreateAndUpload() {
 
 	// useEffect on extractionStatus for preview generation
 	useEffect(async () => {
-		if (extractionStatus !== null && extractionStatus === true) {
+		if (extractionStatus !== null) {
+			setLoadingText(extractionStatus);
 			const clientInfo = await getClientInfo();
 			const file_name = filename.replace(/\.[^/.]+$/, ""); // get filename without extension;
 			const dataset_id = datasets[0].id;
 			// check extraction status and html file generation in loop
 			const html_file_loop = async () => {
-				setLoadingText("Checking extraction status");
 				const highlights_filename = file_name + '_highlights' + '.json'
 				const highlightsFile = await getFileInDataset(dataset_id, "application/json", highlights_filename, clientInfo);
 				if (highlightsFile !== null && typeof highlightsFile.id === "string") {
@@ -86,7 +85,6 @@ export default function CreateAndUpload() {
 					}
 					datasetMetadata(metadata);
 
-					setLoadingText("Extraction completed");
 					setPreview(false)  // Continue button activated
 					setSpinner(false); // stop display of spinner
 				} else {
@@ -102,35 +100,30 @@ export default function CreateAndUpload() {
 			}
 		}
 		else if (extractionStatus === false){
-			setLoadingText("Error in extraction");
+			dispatch(setExtractionStatus("Error in extraction"));
 			setSpinner(false); // stop display of spinner
 		}
-	}, [extractionStatus]);
+	}, [extractionStatus]); // TODO: This useEffect will trigger again when the extractionStatus is completed 
 
 
 	// onDrop function to trigger createUploadExtract action dispatch
 	const onDrop = useCallback((acceptedFiles, rejectedFiles) => {
-		if (!statementTypeSelected) {
-			setLoadingText("Please select a statement type (Trial results or Trial protocol) first");
-			setSpinner(false);
-			return;
-		}
-
+		// this callback function is triggered when a file is dropped into the dropzone
 		setLoading(true);
 		try {
 			acceptedFiles.map(file => {
 				onDropFile(file)
 			})
 			rejectedFiles.map(file => {
-				setLoadingText("File rejected");
+				dispatch(setExtractionStatus("File rejected"));
 				setSpinner(false);
 			})
 		}
 		catch(error) {
-			setLoadingText("Upload failed", error)
+			dispatch(setExtractionStatus("Upload failed"));
 			setSpinner(false);
 		}
-	}, [mouseHover, statementTypeSelected]);
+	}, [mouseHover]);
 
 
 	const goToPreviewRoute = () => {
@@ -144,23 +137,22 @@ export default function CreateAndUpload() {
 		<Box className="createupload">
 			<LoadingOverlay active={loading} text={loading_text} spinner={spinner}>
 				<div className="mousehoverdrop" onMouseEnter={() => setMouseHover(true)}>
-					<Dropfile 
-						onDrop={onDrop} 
+					<Dropfile
+						onDrop={onDrop}
 						accept={{
-							"application/vnd.openxmlformats-officedocument.wordprocessingml.document": [".docx"],  
-							"application/msword": [".doc"], 
+							"application/vnd.openxmlformats-officedocument.wordprocessingml.document": [".docx"],
+							"application/msword": [".doc"],
 							"application/pdf": [".pdf"]
 						}}
-						message={!statementTypeSelected ? 
-							"Please select a statement type above before uploading files" : 
-							"Drag and drop files here"}
+						message={"Drag and drop files here"}
 					/>
 				</div>
 			</LoadingOverlay>
 
 			<div className="radio-buttons-group-div">
-				<RadioGroup 
-					name="radio-buttons-group" 
+				<RadioGroup
+					defaultValue={statementType}
+					name="radio-buttons-group"
 					row
 					onChange={handleStatementChange}
 				>

src/components/childComponents/FilePreview.js

@@ -33,7 +33,7 @@ export default function FilePreview() {
 		if (filePreviews !== undefined && filePreviews.length > 0) {
 			const previewsTemp = [];
 			// get either pdf preview / html preview
-			if (filePreviews.length === 1){
+			if (filePreviews.length > 0){
 				console.log("filePreviews:", filePreviews);
 				const fileId = filePreviews[0][0].file_id;
 				const previewsList = filePreviews[0][0].previews;

src/components/previewers/Pdf.js

@@ -4,91 +4,16 @@ import {useDispatch, useSelector} from "react-redux";
 import { pdfjs , Document, Page } from 'react-pdf';
 import "react-pdf/dist/esm/Page/TextLayer.css";
 import {SET_PAGE_NUMBER, setPageNumber} from "../../actions/pdfpreview";
+import { 
+    consort_highlight_color, 
+    consort_label_color, 
+    spirit_highlight_color, 
+    spirit_label_color 
+} from '../styledComponents/HighlightColors';
 
 
 pdfjs.GlobalWorkerOptions.workerSrc = `//cdnjs.cloudflare.com/ajax/libs/pdf.js/${pdfjs.version}/pdf.worker.js`;
 
-const highlight_color = {
-	"1a":"#88FF88",
-	"1b":"#88FF88",
-	"2a": "#CCAAFF",
-	"2b": "#CCAAFF",
-	"3a": "#88FFFF",
-	"3b": "#88FFFF",
-	"4a": "#88FFFF",
-	"4b": "#88FFFF",
-	"5":  "#88FFFF",
-	"6a": "#88FFFF",
-	"6b": "#88FFFF",
-	"7a": "#88FFFF",
-	"7b": "#88FFFF",
-	"8a": "#88FFFF",
-	"8b": "#88FFFF",
-	"9" : "#88FFFF",
-	"10" :"#88FFFF",
-	"11a" :"#88FFFF",
-	"11b" :"#88FFFF",
-	"12a ":"#88FFFF",
-	"12b" :"#88FFFF",
-	"13a":"#bbff44",
-	"13b" :"#bbff44",
-	"14a" :"#bbff44",
-	"14b" :"#bbff44",
-	"15" :"#bbff44",
-	"16" :"#bbff44",
-	"17a" :"#bbff44",
-	"17b" :"#bbff44",
-	"18" :"#bbff44",
-	"19" :"#bbff44",
-	"20" :"#AACCFF",
-	"21" :"#AACCFF",
-	"22" :"#AACCFF",
-	"23" :"#FFAACC",
-	"24" :"#FFAACC",
-	"25" :"#FFAACC",
-}
-
-const label_color = {
-	"1a":"#009c00",
-	"1b":"#009c00",
-	"2a": "#4400aa",
-	"2b": "#4400aa",
-	"3a": "#009c9c",
-	"3b": "#009c9c",
-	"4a": "#009c9c",
-	"4b": "#009c9c",
-	"5":  "#009c9c",
-	"6a": "#009c9c",
-	"6b": "#009c9c",
-	"7a": "#009c9c",
-	"7b": "#009c9c",
-	"8a": "#009c9c",
-	"8b": "#009c9c",
-	"9" : "#009c9c",
-	"10" :"#009c9c",
-	"11a" :"#009c9c",
-	"11b" :"#009c9c",
-	"12a ":"#009c9c",
-	"12b" :"#009c9c",
-	"13a":"#528100",
-	"13b" :"#528100",
-	"14a" :"#528100",
-	"14b" :"#528100",
-	"15" :"#528100",
-	"16" :"#528100",
-	"17a" :"#528100",
-	"17b" :"#528100",
-	"18" :"#528100",
-	"19" :"#528100",
-	"20" :"#0044aa",
-	"21" :"#0044aa",
-	"22" :"#0044aa",
-	"23" :"#0044aa",
-	"24" :"#0044aa",
-	"25" :"#0044aa",
-}
-
-
 export default function Pdf(props) {
 	const dispatch = useDispatch();
 
@@ -105,6 +30,8 @@ export default function Pdf(props) {
 	let pageNumber = useSelector((state) => state.pdfpreview.pageNumber);
 	const dispatchPageNumber = (number) => dispatch(setPageNumber(SET_PAGE_NUMBER, number));
 
+	const statementType = useSelector(state => state.statement.statementType);
+
 	const [pageWidth, setPageWidth] = useState(500);
 	const [pageHeight, setPageHeight]= useState(799);
 	let [canvas_width, setCanvasWidth] = useState(500);
@@ -197,16 +124,16 @@ export default function Pdf(props) {
 	function highlightText(context, label, x, y, width, height){
 		// rectangle highlights styling
 		context.globalAlpha = 0.2
-		context.fillStyle = highlight_color[label];  // 'rgb(255, 190, 60)';
+		context.fillStyle = statementType === "consort" ? consort_highlight_color[label] : spirit_highlight_color[label];
 		context.fillRect(x , y , width , height );
 	}
 
 	function highlightLabel(context, label, x, y){
 		context.globalAlpha = 1.0
-		context.fillStyle =  highlight_color[label];
+		context.fillStyle = statementType === "consort" ? consort_highlight_color[label] : spirit_highlight_color[label];
 		context.fillRect(x, y, 25, 12);
 		context.font = "bold 12px Verdana";
-		context.fillStyle = label_color[label];
+		context.fillStyle = statementType === "consort" ? consort_label_color[label] : spirit_label_color[label];
 		context.textAlign = "start";
 		context.textBaseline = "top";
 		context.fillText(label, x, y);

src/components/styledComponents/HighlightColors.js

@@ -0,0 +1,187 @@
+export const consort_highlight_color = {
+	"1a":"#88FF88",
+	"1b":"#88FF88",
+	"2a": "#CCAAFF",
+	"2b": "#CCAAFF",
+	"3a": "#88FFFF",
+	"3b": "#88FFFF",
+	"4a": "#88FFFF",
+	"4b": "#88FFFF",
+	"5":  "#88FFFF",
+	"6a": "#88FFFF",
+	"6b": "#88FFFF",
+	"7a": "#88FFFF",
+	"7b": "#88FFFF",
+	"8a": "#88FFFF",
+	"8b": "#88FFFF",
+	"9" : "#88FFFF",
+	"10" :"#88FFFF",
+	"11a" :"#88FFFF",
+	"11b" :"#88FFFF",
+	"12a ":"#88FFFF",
+	"12b" :"#88FFFF",
+	"13a":"#bbff44",
+	"13b" :"#bbff44",
+	"14a" :"#bbff44",
+	"14b" :"#bbff44",
+	"15" :"#bbff44",
+	"16" :"#bbff44",
+	"17a" :"#bbff44",
+	"17b" :"#bbff44",
+	"18" :"#bbff44",
+	"19" :"#bbff44",
+	"20" :"#AACCFF",
+	"21" :"#AACCFF",
+	"22" :"#AACCFF",
+	"23" :"#FFAACC",
+	"24" :"#FFAACC",
+	"25" :"#FFAACC",
+}
+
+export const consort_label_color = {
+	"1a":"#009c00",
+	"1b":"#009c00",
+	"2a": "#4400aa",
+	"2b": "#4400aa",
+	"3a": "#009c9c",
+	"3b": "#009c9c",
+	"4a": "#009c9c",
+	"4b": "#009c9c",
+	"5":  "#009c9c",
+	"6a": "#009c9c",
+	"6b": "#009c9c",
+	"7a": "#009c9c",
+	"7b": "#009c9c",
+	"8a": "#009c9c",
+	"8b": "#009c9c",
+	"9" : "#009c9c",
+	"10" :"#009c9c",
+	"11a" :"#009c9c",
+	"11b" :"#009c9c",
+	"12a ":"#009c9c",
+	"12b" :"#009c9c",
+	"13a":"#528100",
+	"13b" :"#528100",
+	"14a" :"#528100",
+	"14b" :"#528100",
+	"15" :"#528100",
+	"16" :"#528100",
+	"17a" :"#528100",
+	"17b" :"#528100",
+	"18" :"#528100",
+	"19" :"#528100",
+	"20" :"#0044aa",
+	"21" :"#0044aa",
+	"22" :"#0044aa",
+	"23" :"#0044aa",
+	"24" :"#0044aa",
+	"25" :"#0044aa",
+}
+
+export const spirit_highlight_color = {
+	"1": "#AACCFF",
+	"2a": "#AACCFF",
+	"2b": "#AACCFF",
+	"3": "#AACCFF",
+	"4": "#AACCFF",
+	"5a":  "#AACCFF",
+	"5b": "#AACCFF",
+	"5c": "#AACCFF",
+	"5d": "#AACCFF",
+	"6a": "#CCAAFF",
+	"6b": "#CCAAFF",
+	"7": "#CCAAFF",
+	"8": "#CCAAFF",
+	"9" : "#88FFFF",
+	"10" : "#88FFFF",
+	"11a" : "#88FFFF",
+	"11b" : "#88FFFF",
+	"11c" : "#88FFFF",
+	"11d" : "#88FFFF",
+	"12": "#88FFFF",
+	"13": "#88FFFF",
+	"14" : "#88FFFF",
+	"15" : "#88FFFF",
+	"16a" : "#88FFFF",
+	"16b" : "#88FFFF",
+	"16c" : "#88FFFF",
+	"17a" : "#88FFFF",
+	"17b" : "#88FFFF",
+	"18a" : "#88FFFF",
+	"18b" : "#88FFFF",
+	"19" : "#88FFFF",
+	"20a" : "#88FFFF",
+	"20b" : "#88FFFF",
+	"20c" : "#88FFFF",
+	"21a" : "#88FFFF",
+	"21b" : "#88FFFF",
+	"22" : "#88FFFF",
+	"23" : "#88FFFF",
+	"24" : "#bbff44",
+	"25" : "#bbff44",
+	"26a" : "#bbff44",
+	"26b" : "#bbff44",
+	"27" : "#bbff44",
+	"28" : "#bbff44",
+	"29" : "#bbff44",
+	"30" : "#bbff44",
+	"31a" : "#bbff44",
+	"31b" : "#bbff44",
+	"31c" : "#bbff44",
+	"32" : "#FFAACC",
+	"33" : "#FFAACC",
+}
+
+export const spirit_label_color = {
+	"1": "#0044aa",
+	"2a": "#0044aa",
+	"2b": "#0044aa",
+	"3": "#0044aa",
+	"4": "#0044aa",
+	"5a": "#0044aa",
+	"5b": "#0044aa",
+	"5c": "#0044aa",
+	"5d": "#0044aa",
+	"6a": "#4400aa",
+	"6b": "#4400aa",
+	"7": "#4400aa",
+	"8": "#4400aa",
+	"9" : "#009c9c",
+	"10" : "#009c9c",
+	"11a" : "#009c9c",
+	"11b" : "#009c9c",
+	"11c" : "#009c9c",
+	"11d" : "#009c9c",
+	"12": "#009c9c",
+	"13": "#009c9c",
+	"14" : "#009c9c",
+	"15" : "#009c9c",
+	"16a" : "#009c9c",
+	"16b" : "#009c9c",
+	"16c" : "#009c9c",
+	"17a" : "#009c9c",
+	"17b" : "#009c9c",
+	"18a" : "#009c9c",
+	"18b" : "#009c9c",
+	"19" : "#009c9c",
+	"20a" : "#009c9c",
+	"20b" : "#009c9c",
+	"20c" : "#009c9c",
+	"21a" : "#009c9c",
+	"21b" : "#009c9c",
+	"22" : "#009c9c",
+	"23" : "#009c9c",
+	"24" : "#528100",
+	"25" : "#528100",
+	"26a" : "#528100",
+	"26b" : "#528100",
+	"27" : "#528100",
+	"28" : "#528100",
+	"29" : "#528100",
+	"30" : "#528100",
+	"31a" : "#528100",
+	"31b" : "#528100",
+	"31c" : "#528100",
+	"32" : "#0044aa",
+	"33" : "#0044aa",
+} 

src/utils/dataset.js

@@ -206,26 +206,26 @@ export async function setDatasetMetadata(dataset_id, content) {
 export async function getDatasetMetadataLoop(dataset_id, extractor_name, clientInfo){
 	/**
 	 * Asynchronously retrieves dataset metadata by repeatedly checking until it's available.
-	 * 
+	 *
 	 * @param {string} dataset_id - The ID of the dataset to retrieve metadata for.
 	 * @param {string} extractor_name - The name of the extractor used (currently unused in the function).
 	 * @param {Object} clientInfo - Client information required for API calls.
 	 * @returns {Promise<Object|Array>} The dataset metadata content if successful, or an empty array if unsuccessful.
-	 * 
+	 *
 	 * This function implements a polling mechanism to check for dataset metadata:
 	 * 1. It attempts to retrieve the metadata using the provided dataset ID and client info.
 	 * 2. If metadata is available, it returns the content of the first metadata item.
 	 * 3. If metadata is not yet available, it waits for 30 seconds before trying again.
 	 * 4. This process repeats until metadata is found or an error occurs.
-	 * 
+	 *
 	 */
-	
+
 	const extractor_metadata_loop = async () => {
 		// get dataset metadata as json-ld
 		const metadata = await getDatasetMetadata(dataset_id, clientInfo);
 		if (metadata !== null && metadata.length > 0) {
 			// Filter metadata for the specified extractor
-			const relevantMetadata = metadata.filter(item => 
+			const relevantMetadata = metadata.filter(item =>
 				item.content && item.content.extractor === extractor_name
 			);
 
@@ -235,13 +235,13 @@ export async function getDatasetMetadataLoop(dataset_id, extractor_name, clientI
 				return relevantMetadata[0].content;
 			} else {
 				console.log(`No metadata found for extractor: ${extractor_name}`);
-				console.log("Waiting 30 seconds before checking again...");
-				await sleep(30000);
+				console.log("Waiting 5 seconds before checking again...");
+				await sleep(5000);
 				return await extractor_metadata_loop();
 			}
 		} else {
-			console.log("check for extraction metadata after 30s");
-			await sleep(30000);
+			console.log("check for extraction metadata after 5s");
+			await sleep(5000);
 			await extractor_metadata_loop();
 		}
 	};