Merge pull request #929 from BV-BRC/beta

1/31/2025 release
BV-BRC · Feb 3, 2025 · 18336f2 · 18336f2
2 parents 7088c93 + 5071d66
commit 18336f2
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Showing 18 changed files with 520 additions and 138 deletions.
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "p3-web",
-  "version": "3.45.4",
+  "version": "3.46.3",
   "private": true,
   "scripts": {
     "start": "node ./bin/p3-web",

diff --git a/public/js/p3/resources/assembly.css b/public/js/p3/resources/assembly.css
@@ -1,5 +1,5 @@
 .appTemplate {
-    width: 750px;
+    max-width: 750px;
     margin: auto;
 }
 

diff --git a/public/js/p3/widget/DownloadTooltipDialog.js b/public/js/p3/widget/DownloadTooltipDialog.js
@@ -230,14 +230,27 @@ define([
       domConstruct.create('div', { 'class': 'wsActionTooltip', rel: 'csv', innerHTML: 'CSV' }, tData);
       // domConstruct.create("div", {"class": "wsActionTooltip", rel: "excel", innerHTML: "Excel"}, tData);
 
-      tr = domConstruct.create('tr', {}, table);
-      var td = domConstruct.create('td', { colspan: 3, style: 'text-align:right' }, tr);
-      this.advancedDownloadButton = domConstruct.create('span', {
-        'class': 'wsActionTooltip',
-        style: 'padding:4px;',
-        rel: 'advancedDownload',
-        innerHTML: 'More Options'
-      }, td);
+      if (this.isGenomeOverview) {
+        const conf = this.downloadableConfig[this.containerType] || this.downloadableConfig['default'];
+        if (conf && conf.otherData) {
+          conf.otherData.forEach(function (type) {
+            domConstruct.create('div', {
+              'class': 'wsActionTooltip',
+              rel: type,
+              innerHTML: this.downloadableDataTypes[type]
+            }, this.otherDownloadNode);
+          }, this);
+        }
+      } else {
+        tr = domConstruct.create('tr', {}, table);
+        var td = domConstruct.create('td', {colspan: 3, style: 'text-align:right'}, tr);
+        this.advancedDownloadButton = domConstruct.create('span', {
+          'class': 'wsActionTooltip',
+          style: 'padding:4px;',
+          rel: 'advancedDownload',
+          innerHTML: 'More Options'
+        }, td);
+      }
 
       this.set('content', dstContent);
 
@@ -250,7 +263,7 @@ define([
     _setLabelAttr: function (val) {
       this.label = val;
       if (this._started) {
-        this.labelNode.innerHTML = 'Download selected ' + val + ' (' + (this.selection ? this.selection.length : '0') + ') as...';
+        this.labelNode.innerHTML = this.isGenomeOverview ? 'Download options' : 'Download selected ' + val + ' (' + (this.selection ? this.selection.length : '0') + ') as...';
       }
     },
 

diff --git a/public/js/p3/widget/GenomeOverview.js b/public/js/p3/widget/GenomeOverview.js
@@ -3,15 +3,15 @@ define([
   'dojo/dom-class', 'dojo/query', 'dojo/dom-style', 'dojo/text!./templates/GenomeOverview.html', 'dojo/dom-construct',
   'dijit/_WidgetBase', 'dijit/_TemplatedMixin', 'dijit/_WidgetsInTemplateMixin', 'dijit/Dialog',
   '../util/PathJoin', './SelectionToGroup', './GenomeFeatureSummary', './DataItemFormatter',
-  './ExternalItemFormatter', './AdvancedDownload', 'dijit/form/TextBox', 'dijit/form/Form', './Confirmation',
+  './ExternalItemFormatter', './DownloadTooltipDialog', 'dijit/form/TextBox', 'dijit/form/Form', './Confirmation',
   './InputList', 'dijit/form/SimpleTextarea', 'dijit/form/DateTextBox', './MetaEditor',
   '../DataAPI', './PermissionEditor', './ServicesTooltipDialog', 'dijit/popup'
 ], function (
   declare, lang, on, xhr, Topic,
   domClass, domQuery, domStyle, Template, domConstruct,
   WidgetBase, Templated, _WidgetsInTemplateMixin, Dialog,
   PathJoin, SelectionToGroup, GenomeFeatureSummary, DataItemFormatter,
-  ExternalItemFormatter, AdvancedDownload, TextBox, Form, Confirmation,
+  ExternalItemFormatter, DownloadTooltipDialog, TextBox, Form, Confirmation,
   InputList, TextArea, DateTextBox, MetaEditor,
   DataAPI, PermissionEditor, ServicesTooltipDialog, popup
 ) {
@@ -249,10 +249,16 @@ define([
     },
 
     onDownload: function () {
-      var dialog = new Dialog({ title: 'Download' });
-      var advDn = new AdvancedDownload({ selection: [this.genome], containerType: 'genome_data' });
-      domConstruct.place(advDn.domNode, dialog.containerNode);
-      dialog.show();
+      popup.open({
+        popup: new DownloadTooltipDialog({
+          selection: [this.genome],
+          containerType: 'genome_data',
+          isGenomeOverview: true
+        }),
+        parent: this,
+        around: this.genomeDownloadButton,
+        orient: ['below']
+      });
     },
 
     onClickUserGuide: function () {

diff --git a/public/js/p3/widget/RerunUtility.js b/public/js/p3/widget/RerunUtility.js
@@ -42,7 +42,8 @@ define([], function () {
         'HASubtypeNumberingConversion': 'HASubtypeNumberingConversion',
         'TaxonomicClassification': 'TaxonomicClassification',
         'TnSeq': 'Tnseq',
-        'Variation': 'Variation'
+        'Variation': 'Variation',
+        'ViralAssembly': 'ViralAssembly'
       };
 
       // TODO: addin modal parameter

diff --git a/public/js/p3/widget/WorkspaceBrowser.js b/public/js/p3/widget/WorkspaceBrowser.js
@@ -1229,6 +1229,22 @@ define([
         }
       }, false);
 
+      this.browserHeader.addAction('ViewViralAssemblyReport', 'fa icon-eye fa-2x', {
+        label: 'Report',
+        multiple: false,
+        validTypes: ['ViralAssembly'],
+        tooltip: 'View Viral Assembly Report'
+      }, function (selection) {
+        const path = selection[0].autoMeta.output_files.find(meta_file_data =>
+          meta_file_data[0].includes('AssemblyReport.html')
+        );
+        if (path && path[0]) {
+          Topic.publish('/navigate', { href: '/workspace' + encodePath(path[0]) });
+        } else {
+          console.log('Error: could not find AssemblyReport.html output file');
+        }
+      }, false);
+
       this.browserHeader.addAction('ViewHASubtypeNumberingReport', 'fa icon-eye fa-2x', {
         label: 'Report',
         multiple: false,

diff --git a/public/js/p3/widget/app/Docking.js b/public/js/p3/widget/app/Docking.js
@@ -85,34 +85,36 @@ define([
     },
 
     onInputChange: function (evt) {
-      // protein radio buttons
-      if (this.protein_databank_selection.checked) {
-        // set display logic
-        dojo.style(this.block_pdb_list, "display", "block");
-        dojo.style(this.block_pdb_upload, "display", "none");
-      }
-      else if (this.user_pdb_file.checked) {
-        dojo.style(this.block_pdb_list, "display", "none");
-        dojo.style(this.block_pdb_upload, "display", "block");
-      }
-      // ligand radio buttons
-      if (this.input_sequence.checked)
-      {
-        dojo.style(this.block_smiles_text, 'display', 'block');
-        dojo.style(this.block_smiles_ws, 'display', 'none');
-        dojo.style(this.block_smiles_dropdown, 'display', 'none');
-      }
-      else if (this.ws_file.checked)
-      {
-        dojo.style(this.block_smiles_text, 'display', 'none');
-        dojo.style(this.block_smiles_ws, 'display', 'block');
-        dojo.style(this.block_smiles_dropdown, 'display', 'none');
-      }
-      else if (this.ligand_named_library.checked)
+      if (typeof this.protein_databank_selection != "undefined"){
+        // protein radio buttons
+        if (this.protein_databank_selection.checked) {
+          // set display logic
+          dojo.style(this.block_pdb_list, "display", "block");
+          dojo.style(this.block_pdb_upload, "display", "none");
+        }
+        else if (this.user_pdb_file.checked) {
+          dojo.style(this.block_pdb_list, "display", "none");
+          dojo.style(this.block_pdb_upload, "display", "block");
+        }
+        // ligand radio buttons
+        if (this.input_sequence.checked)
+        {
+          dojo.style(this.block_smiles_text, 'display', 'block');
+          dojo.style(this.block_smiles_ws, 'display', 'none');
+          dojo.style(this.block_smiles_dropdown, 'display', 'none');
+        }
+        else if (this.ws_file.checked)
         {
-        dojo.style(this.block_smiles_text, 'display', 'none');
-        dojo.style(this.block_smiles_ws, 'display', 'none');
-        dojo.style(this.block_smiles_dropdown, 'display', 'block');
+          dojo.style(this.block_smiles_text, 'display', 'none');
+          dojo.style(this.block_smiles_ws, 'display', 'block');
+          dojo.style(this.block_smiles_dropdown, 'display', 'none');
+        }
+        else if (this.ligand_named_library.checked)
+          {
+          dojo.style(this.block_smiles_text, 'display', 'none');
+          dojo.style(this.block_smiles_ws, 'display', 'none');
+          dojo.style(this.block_smiles_dropdown, 'display', 'block');
+        }
       }
       },
 
@@ -130,7 +132,7 @@ define([
     "pdb_preview": "",
     "input": "smiles_list",
     "smiles_text": "asdfasdf",
-    "smiles_ws_file": "",
+    "ligand_ws_file": "",
     "output_path": "/olson@patricbrc.org/home/test/test1/test2",
     "output_file": "abc"
 } */
@@ -179,7 +181,7 @@ define([
       }
       else if (values.input === 'ws_file')
       {
-        submit_values.ligand_ws_file = values.smiles_ws_file;
+        submit_values.ligand_ws_file = values.ligand_ws_file;
       }
       else if (values.input === 'named_library')
       {
@@ -201,7 +203,7 @@ define([
         }
       }
     },
-    
+
     onOutputPathChange: function (val) {
       this.inherited(arguments);
       this.checkParameterRequiredFields();
@@ -213,13 +215,25 @@ define([
     },
 
     addRerunFields: function (job_params) {
-      var ligand_library_type = job_params['ligand_library_type']; 
+      // Protein Input
+      if (job_params.protein_input_type === 'user_pdb_file'){
+        this.protein_databank_selection.set('checked', false);
+        this.user_pdb.set('value', job_params["user_pdb_file"])
+        this.user_pdb_file.set('checked', true);
+      }
+      else if (job_params.protein_input_type === 'input_pdb'){
+        this.pdb_list.set('value', job_params["input_pdb"]);
+      }
+      else {
+        console.log( 'Invalid protein input');
+      }
+      // ligand library is not working just yet
+      var ligand_library_type = job_params['ligand_library_type'];
       if (ligand_library_type === "ws_file"){
         this.ws_file.checked
         this.ws_file.set('value', ligand_library_type);
-        this.smiles_ws_file.set('value', job_params['ligand_ws_file']);
-
-        } 
+        this.ligand_ws_file.set('value', job_params['ligand_ws_file']);
+      } 
       else if (ligand_library_type === "smiles_list"){
         this.input_sequence.checked;
         this.input_sequence.set('value', ligand_library_type);
@@ -234,15 +248,13 @@ define([
       else if (ligand_library_type === "named_library"){
         this.ligand_named_library.checked;
         this.ligand_named_library.set('value', ligand_library_type);
-        this.smiles_dropdown.set('value', job_params['ligand_named_library'])
-        this.ligand_named_library.set('value', job_params['ligand_named_library']);
+        this.smiles_dropdown_attach_point.set('value', job_params['ligand_named_library']);
       } 
-      else{
+      else {
         console.log("Improper ligand library type passed.")
       }
-      this.pdb_list.set('value', job_params["input_pdb"]);
       this.output_path.set('value', job_params['output_path']);
-    },
+      },
 
     intakeRerunForm: function () {
       // assuming only one key
@@ -269,4 +281,3 @@ define([
     }
   });
 });
-