Added the ability to edit the contents of the metadata component tabl…

…e along with the ability to export in .tsv format. Added a link to publications in the disclaimer.

index.html

@@ -304,7 +304,7 @@ <h3 class="card-title" data-i18n-key="legend">Legend</h3>
       <div class="footer-info">
         <div class="info">
           <p><span data-i18n-key="cookies_notice">Questa applicazione non utilizza cookies.</span></p>
-          <p><span data-i18n-key="last_updated_on">Last updated on</span> <span class="last-update-date">2024-05-07</span></p>
+          <p><span data-i18n-key="last_updated_on">Last updated on</span> <span class="last-update-date">__LAST_UPDATE__</span></p>
           <p class="copyright">&copy; <span class="copyright-year"></span> IZSAM 'G. Caporale'</p>
         </div>
       </div>

js/file-handler.js

@@ -370,7 +370,8 @@ gtiz_file_handler.parseMetadata = function(msg, lines, header_index) {
 	}
 	let meta = {};
 	let id_name = '';
-	let category = 'nothing';
+	let tree = gtiz_tree.tree;
+	let category = tree.display_category ? tree.display_category : 'nothing';
 	let options = {};
 	if (header_index) {
 		if (header_index.find(function(d) {return d == "ID"})) {
@@ -379,7 +380,9 @@ gtiz_file_handler.parseMetadata = function(msg, lines, header_index) {
 			id_name = header_index[0];
 		}
 		gtiz_file_handler.samples_column = id_name;
-		category = header_index.length > 1 ? header_index[1] : header_index[0];
+		if (category == 'nothing') {
+			category = header_index.length > 1 ? header_index[1] : header_index[0];
+		}
 		for (let i in header_index) {
 			let header = header_index[i];
 			options[header] = header;

js/i18n/en.js

@@ -148,6 +148,7 @@ gtiz_languages.en = {
   "original_tree": "Original tree",
   "pie_chart_mode": "Pie Chart mode",
   "possible_performance_issues_message" : "Possible performance issues, I suggest to set link distances value to <strong>{0}</strong>.",
+  "publications": "Publications",
   "quick_gradient": "Quick gradient",
   "radius_size": "Radius size (%)",
   "real_branch_length" : "Real branch length",

js/i18n/it.js

@@ -148,6 +148,7 @@ gtiz_languages.it = {
   "original_tree": "Tree iniziale",
   "pie_chart_mode": "Modalità diagramma",
   "possible_performance_issues_message" : "Potresti avere problemi di performance visualizzando il tree esteso. Suggerisco di impostare la distanza dei collegamenti su <strong>{0}</strong>.",
+  "publications": "Pubblicazioni",
   "quick_gradient": "Gradiente veloce",
   "radius_size": "Dimensione raggio (%)",
   "real_branch_length" : "Lunghezza branch reale",

js/languages.js

@@ -153,6 +153,7 @@ gtiz_languages.en = {
   "original_tree": "Original tree",
   "pie_chart_mode": "Pie Chart mode",
   "possible_performance_issues_message" : "Possible performance issues, I suggest to set link distances value to <strong>{0}</strong>.",
+  "publications": "Publications",
   "quick_gradient": "Quick gradient",
   "radius_size": "Radius size (%)",
   "real_branch_length" : "Real branch length",
@@ -284,7 +285,7 @@ gtiz_languages.it = {
   "export_newick" : "Esporta newick",
   "fetch_error" : "La richiesta di caricamento del file non è riuscita.",
   "font_size" : "Dimensione carattere",
-  "footer_disclaimer" : "Questo progetto fa parte dell'European Joint Programme One Health EJP. Il progetto ha ricevuto finanziamenti dal programma di ricerca e innovazione Horizon 2020 dell'Unione europea nell'ambito del Grant Agreement No 773830.",
+  "footer_disclaimer" : "Questo progetto fa parte dell'European Joint Programme One Health EJP. Il progetto ha ricevuto finanziamenti dal programma di ricerca e innovazione Horizon 2020 dell'Unione Europea nell'ambito del Grant Agreement No 773830.",
   "for_branches_longer_than" : "Per collegamenti più lunghi di:",
   "forbidden_net_geojson_alert" : "Sembra che tu non abbia i permessi per accedere al GeoJson indicato nella URL. Prova a fare la login su <a href='{0}' target='_blank'>{1}</a> ed aggiorna la pagina.",
   "forbidden_net_metadata_alert" : "Sembra che tu non abbia i permessi per accedere ai Metadata indicati nella URL. Prova a fare la login su <a href='{0}' target='_blank'>{1}</a> ed aggiorna la pagina.",
@@ -389,6 +390,7 @@ gtiz_languages.it = {
   "original_tree": "Tree iniziale",
   "pie_chart_mode": "Modalità diagramma",
   "possible_performance_issues_message" : "Potresti avere problemi di performance visualizzando il tree esteso. Suggerisco di impostare la distanza dei collegamenti su <strong>{0}</strong>.",
+  "publications": "Pubblicazioni",
   "quick_gradient": "Gradiente veloce",
   "radius_size": "Dimensione raggio (%)",
   "real_branch_length" : "Lunghezza branch reale",

js/metadata.js

@@ -138,6 +138,15 @@ gtiz_metadata.context_menu = [{
   function : () => {
     gtiz_metadata.downloadCsv();
   }
+}, {
+  type : 'button',
+  label : () => {
+    return gtiz_locales.current.download_table + ' (.tsv)';
+  },
+  icon : 'iconic-file-text',
+  function : () => {
+    gtiz_metadata.downloadTsv();
+  }
 }];
 
 
@@ -285,6 +294,33 @@ gtiz_metadata.getColorByOptions = function() {
   return colors;
 }
 
+/**
+ * Export table as tsv
+ * 
+ * 
+ */
+gtiz_metadata.downloadTsv = function() {
+  let nodes = gtiz_metadata.options.api.getRenderedNodes();
+  let array = [];
+  nodes.forEach(element => {
+    if (element.data.nothing) {
+      delete element.data.nothing;   
+    }
+    array.push(element.data);
+  });
+  let keys = Object.keys(array[0]);
+  // Create the header row
+  let tsv = keys.join('\t') + '\n';
+  // Create the data rows
+  for (let obj of array) {
+      let values = Object.values(obj);
+      tsv += values.join('\t') + '\n';
+  }
+  let timestamp =  Date.now();
+  let name = "metadata" + timestamp + ".tsv";
+  gtiz_file_handler.saveTextAsFile(tsv, name);
+}
+
 /**
  * Export table as csv
  * 
@@ -295,8 +331,11 @@ gtiz_metadata.downloadCsv = function() {
   let columns = gtiz_metadata.options.columnApi.getColumns();
   // we are removing first column dedicated to checkbox
   columns.shift();
+  let timestamp =  Date.now();
+  let name = "metadata" + timestamp + ".csv";
   gtiz_metadata.options.api.exportDataAsCsv({
-    columnKeys: columns
+    columnKeys: columns,
+    fileName: name
   });
 }
 
@@ -467,6 +506,44 @@ gtiz_metadata.options = {
   doesExternalFilterPass: (node) => {
     let filtered = gtiz_metadata.doesExternalFilterPass(node);
     return filtered;
+  },
+  onCellValueChanged: (event) => {
+    console.log(event);
+
+    let nodes = gtiz_metadata.options.api.getRenderedNodes();
+    let array = [];
+    nodes.forEach(element => {
+      if (element.data.nothing) {
+        delete element.data.nothing;   
+      }
+      array.push(element.data);
+    });
+    let keys = Object.keys(array[0]);
+    // Create the header row
+    let tsv = keys.join('\t') + '\n';
+    // Create the data rows
+    for (let obj of array) {
+        let values = Object.values(obj);
+        tsv += values.join('\t') + '\n';
+    }
+
+    gtiz_tree.current_metadata_file = tsv;
+		if (gtiz_tree.tree) {
+			let l_action = 'add';
+			let l_components = ['tree', 'map', 'legend'];
+			gtiz_layout.uiLoadingManager(l_components, l_action);
+			gtiz_file_handler.loadMetadataText(tsv);
+			gtiz_map.init();
+		} else {
+			let title = gtiz_locales.current.oops;
+			let contents = [];
+			let body = document.createElement('div');
+			body.innerHTML = gtiz_locales.current.missing_tree_alert;
+			contents.push(body);
+			gtiz_modal.buildModal(title, contents);
+			console.log(gtiz_locales.current.missing_tree_alert);
+		}
+
   }
 };
 
@@ -494,15 +571,15 @@ gtiz_metadata.setGrid = function() {
   columns.push(check);
   Object.keys(fields).forEach((key, index) => {
     if (fields[key] != 'nothing') {
-      let check = fields[key] == 'ID' ? true : false;
       let obj = {};
-      if (check) {
+      if (fields[key] == 'ID' || fields[key] == gtiz_file_handler.samples_column) {
         obj = {
           field : fields[key]
         }
       } else {
         obj = {
-          field : fields[key]
+          field : fields[key],
+          editable: true
         }
       }
       columns.push(obj);

themes/cohesive/html/footer.html

@@ -10,6 +10,7 @@
 <div class="useful useful-links">
   <h6 data-i18n-key="useful_links">Useful links</h6>
   <ul>
+    <li><a href="https://github.com/genpat-it/spread/wiki/Publications" target="_blank" data-i18n-key="publications">Publications</a></li>
     <li><a href="https://onehealthejp.eu/">One Heakth EJP</a></li>
     <li><a href="https://www.izs.it/IZS/Eccellenza/Centri_nazionali/CRN_-_Sequenze_Genomiche" target="_blank"><span data-i18n-key="crn_genome_sequencing">CRN Genome Sequencing</span></a></li>
     <li><a href="https://github.com/achtman-lab/GrapeTree" target="_blank">GrapeTree Github</a></li>

themes/default/html/footer.html

@@ -5,6 +5,7 @@
 <div class="useful useful-links">
   <h6 data-i18n-key="useful_links">Useful links</h6>
   <ul>
+    <li><a href="https://github.com/genpat-it/spread/wiki/Publications" target="_blank" data-i18n-key="publications">Publications</a></li>
     <li><a href="https://github.com/achtman-lab/GrapeTree" target="_blank">GrapeTree Github</a></li>
     <li><a href="https://www.izs.it/IZS/Eccellenza/Centri_nazionali/CRN_-_Sequenze_Genomiche" target="_blank"><span data-i18n-key="crn_genome_sequencing">CRN Genome Sequencing</span></a></li>
     <li><a href="https://www.izs.it/IZS/" target="_blank">IZSAM 'G. Caporale'</a></li>

themes/genpat/html/footer.html

@@ -5,6 +5,7 @@
 <div class="useful useful-links">
   <h6 data-i18n-key="useful_links">Useful links</h6>
   <ul>
+    <li><a href="https://github.com/genpat-it/spread/wiki/Publications" target="_blank" data-i18n-key="publications">Publications</a></li>
     <li><a href="https://github.com/achtman-lab/GrapeTree" target="_blank">GrapeTree Github</a></li>
     <li><a href="https://www.izs.it/IZS/Eccellenza/Centri_nazionali/CRN_-_Sequenze_Genomiche" target="_blank"><span data-i18n-key="crn_genome_sequencing">CRN Genome Sequencing</span></a></li>
     <li><a href="https://www.izs.it/IZS/" target="_blank">IZSAM "G. Caporale"</a></li>