Merge pull request #665 from inab/658-evaluator-unable-to-run-tool-wh…

…en-using-metadata-file-url-or-upload-as-input

658 evaluator unable to run tool when using metadata file url or upload as input

components/observatory/evaluation/MetadataFile/MetadataFileURL.vue

@@ -84,8 +84,8 @@ export default {
 		},
 		exampleValues: [
 			{
-				title: 'FAIRsoft-indicators',
-				URL: 'https://raw.githubusercontent.com/EvaMart/FAIRsoft-indicators/master/FAIRsoft-indicators.metadata.jsonld',
+				title: 'oeb-visualizations',
+				URL: 'https://raw.githubusercontent.com/inab/oeb-visualizations/refs/heads/main/metadata.jsonld',
 			},
 		],
 		installDialogParameters: {
@@ -96,40 +96,12 @@ export default {
 
 	methods: {
 		submitURL() {
-			this.payload = this.ParseGitHubURL(this.URL);
-			if (this.payload) {
-				this.submitGitHubLink();
-			} else {
-				this.$store.dispatch(
-					'observatory/evaluation/file/parseFromURL',
-					this.URL
-				);
-			}
+			this.$store.dispatch('observatory/evaluation/file/downloadFile', {
+				url: this.URL,
+			});
 
 			this.$store.dispatch('observatory/evaluation/changeStep', 3);
 		},
-		ParseGitHubURL(url) {
-			/*
-            Check if the URL is a raw GitHub URL:
-                raw.githubusercontent.com/${user}/${repo}/${branch}/${path}
-            If it is, return the payload to fetch the file content.
-            Else, return null.
-            */
-			const pattern = /^(http(s?):\/\/)?raw\.githubusercontent\.com\/(.*)$/i;
-			if (pattern.test(url)) {
-				const payload = {
-					repo: url.split('/')[4],
-					owner: url.split('/')[3],
-					branch: url.split('/')[5],
-					path: url.split('/').slice(6).join('/'),
-				};
-
-				return payload;
-			} else {
-				return null;
-			}
-		},
-
 		cancel() {
 			this.$store.dispatch(
 				'observatory/evaluation/file/updateDialogInstallApp',
@@ -141,69 +113,6 @@ export default {
 			);
 		},
 
-		async submitGitHubLink() {
-			/*
-            This function is called when the URL introduced by the user is a github one.
-            It checks if the app is installed in the repository and, if it is, fetches the metadata.
-            If it is not installed, it opens a dialog to install it.
-            */
-
-			// 1.1 Open dialog to show progress
-
-			this.$store.dispatch('observatory/evaluation/github/updateRepository', {
-				owner: this.payload.owner,
-				repo: this.payload.repo,
-			});
-
-			this.$store.dispatch(
-				'observatory/evaluation/file/updateDialogParseMetadata',
-				true
-			);
-			console.log('open dialog');
-
-			// 1.2 Get installation ID
-			console.log('Get installation ID');
-			await this.$store.dispatch(
-				'observatory/evaluation/github/getInstallationID',
-				{
-					owner: this.payload.owner,
-					repo: this.payload.repo,
-				}
-			);
-
-			const installationID =
-				this.$store.getters['observatory/evaluation/github/getInstallationID'];
-			console.log('installation ID: ' + installationID);
-
-			// 2. If it is installed, fetch file content
-			if (installationID) {
-				const payload = {
-					installationID,
-					repo: this.payload.repo,
-					owner: this.payload.owner,
-					path: this.payload.path,
-				};
-
-				this.$store.dispatch(
-					'observatory/evaluation/file/parseFromGitHubURL',
-					payload
-				);
-			} else {
-				// 3. If it is not installed, open dialog to install it
-				this.$store.dispatch(
-					'observatory/evaluation/file/updateDialogParseMetadata',
-					false
-				);
-				this.$store.dispatch(
-					'observatory/evaluation/file/updateDialogInstallApp',
-					true
-				);
-
-				// this.$store.dispatch('evaluation/changeLoading', { github : false}) // close loading dialog
-				// this.dialogAppNotInstalled = true // open "app installation" dialog
-			}
-		},
-
 		goBack() {
 			this.$store.dispatch('observatory/evaluation/changeStep', 1);
 			this.value = '';

components/observatory/evaluation/Results/MetadataActions.vue

@@ -8,10 +8,20 @@
 					previous step. It is in JSON-LD format and incorporates
 					<a href="https://schema.org/" target="_blank">Schema.org</a>,
 					<a href="https://bioschemas.org/" target="_blank">Bioschemas</a>, and
-					<a href="" target="_blank">maSMP</a>
+					<a href="https://zbmed-semtec.github.io/maSMPs/" target="_blank"
+						>maSMP</a
+					>
 					entities. This ensures your metadata is highly interoperable on the
 					internet, making it easy to be understood and utilized by a wide range
-					of systems and services.
+					of systems and services. Additionally, this metadata can be used to
+					pre-fill an
+					<a href="https://osf.io/preprints/biohackrxiv/k8znb" target="_blank"
+						>ELIXIR software management plan</a
+					>
+					for your software in the
+					<a href="https://smw.dsw.elixir-europe.org/wizard/" target="_blank"
+						>Software Management Wizard (SMW)</a
+					>.
 				</p>
 				<p>
 					Below, you have several options to preview, download, or directly

plugins/githubapp.js

@@ -10,9 +10,9 @@ export default function ({ $axios, $config: { GITHUBAPP_API_URL } }, inject) {
 
 	// Set baseURL to something different
 	// githubapp.setBaseURL('https://observatory-dev.openebench.bsc.es/github-metadata-api');
+	// githubapp.setBaseURL('http://localhost:3800');
 
 	githubapp.setBaseURL(GITHUBAPP_API_URL);
-	// githubapp.setBaseURL('http://localhost:3500');
 
 	// Inject to context as $api
 	inject('githubapp', githubapp);

plugins/observatory.js

@@ -9,9 +9,10 @@ export default function ({ $axios, $config: { OBSERVATORY_API_URL } }, inject) {
 	});
 
 	// Set baseURL to something different
-	observatory.setBaseURL(OBSERVATORY_API_URL);
 	// observatory.setBaseURL('http://0.0.0.0:3500');
 
+	observatory.setBaseURL(OBSERVATORY_API_URL);
+
 	// Inject to context as $api
 	inject('observatory', observatory);
 }

store/observatory/evaluation/file.js

@@ -322,7 +322,7 @@ export const actions = {
 		if (response) {
 			const fileContent = response.content;
 
-			dispatch('parseMetadataFile', fileContent);
+			dispatch('mapMetadata', fileContent);
 		} else {
 			commit('setErrorDialogParseMetadata', true);
 			commit(
@@ -345,7 +345,8 @@ export const actions = {
 
 			const fileContent = response.data;
 			console.debug('Downloaded file content:', fileContent);
-			await dispatch('parseMetadataFile', JSON.stringify(fileContent));
+			parsedContent = JSON.parse(fileContent);
+			dispatch('mapMetadata', parsedContent);
 		} catch (error) {
 			console.error('Error fetching or parsing file from URL:', error);
 			commit('setErrorDialogParseMetadata', true);
@@ -395,6 +396,42 @@ export const actions = {
 		});
 	},
 
+	async downloadFile({ commit, dispatch }, payload) {
+		commit('setParseProgressText', 'Downloading file from URL...');
+		commit('setDialogParseMetadata', true);
+
+		try {
+			const URL = '/downloads/download-content/';
+
+			const data = {
+				url: payload.url,
+			};
+
+			console.log(data);
+
+			const response = await this.$observatory.post(URL, data, {
+				headers: {
+					'Content-Type': 'application/json',
+				},
+			});
+
+			let fileContent = response.data.content;
+			fileContent = fileContent.trim();
+			fileContent = JSON.parse(fileContent);
+
+			console.log('name', fileContent['schema:name']);
+			await dispatch('mapMetadata', fileContent);
+			console.debug('Downloaded file content:', fileContent);
+		} catch (error) {
+			console.error('Error fetching or parsing file from URL:', error);
+			commit('setErrorDialogParseMetadata', true);
+			commit(
+				'setErrorProgressText',
+				`Error fetching file from URL: ${error.message}`
+			);
+		}
+	},
+
 	async parseMetadataFile({ commit, dispatch }, file) {
 		commit('setParseProgressText', 'Parsing metadata file content...');
 		commit('setDialogParseMetadata', true);
@@ -419,8 +456,10 @@ export const actions = {
 		fileContent = fileContent.trim();
 
 		let parsedContent;
+
 		try {
 			parsedContent = JSON.parse(fileContent);
+			dispatch('mapMetadata', parsedContent);
 		} catch (error) {
 			console.error('Error parsing JSON:', error);
 			commit('setDialogParseMetadata', false);
@@ -432,9 +471,10 @@ export const actions = {
 				'</pre>';
 			commit('setErrorProgressText', errorMessage);
 			dispatch('observatory/evaluation/changeStep', 2, { root: true });
-			return;
 		}
+	},
 
+	mapMetadata({ commit, dispatch }, parsedContent) {
 		// Transform file fields into the UI metadata model fields
 		let metadata = {
 			topics: buildFeTopicsOperations(

store/observatory/evaluation/github.js

@@ -82,6 +82,7 @@ export const actions = {
 			commit('setExtractorInstallationID', installationID);
 		} catch (error) {
 			console.debug('Error while getting installation ID: ' + error);
+			commit('setExtractorInstallationID', null);
 			commit(
 				'setImportProgressText',
 				"error while fetching the repositorie's installation ID for app metadata extractor for FAIRsoft"