Release 6.1.0

package.json

@@ -1,14 +1,14 @@
 {
   "name": "tdp_core",
   "description": "Target discovery platform for exploring rankings of genes, disease models, and other entities.",
-  "version": "6.0.0",
+  "version": "6.1.0",
   "author": {
     "name": "datavisyn",
     "email": "contact@datavisyn.io",
-    "url": "https://datavisyn.io/"
+    "url": "https://www.datavisyn.io"
   },
   "license": "BSD-3-Clause",
-  "homepage": "https://phovea.caleydo.org",
+  "homepage": "https://www.datavisyn.io",
   "bugs": {
     "url": "https://github.com/datavisyn/tdp_core/issues"
   },
@@ -105,7 +105,7 @@
     "karma-sourcemap-loader": "0.3.7",
     "karma-webpack": "2.0.3",
     "mkdirp": "0.5.1",
-    "node-sass": "4.7.2",
+    "node-sass": "^4.12.0",
     "null-loader": "0.1.1",
     "raw-loader": "0.5.1",
     "sass-loader": "6.0.7",

src/ATDPApplication.ts

@@ -136,7 +136,7 @@ export abstract class ATDPApplication<T> extends ACLUEWrapper {
       if (typeof this.options.showResearchDisclaimer === 'function') {
         this.options.showResearchDisclaimer(aboutDialogBody);
       } else {
-        aboutDialogBody.insertAdjacentHTML('afterbegin', '<div class="alert alert-warning" role="alert"><strong>Disclaimer</strong> This software is <strong>for research purpose only</strong>.</span></div>');
+        aboutDialogBody.insertAdjacentHTML('afterbegin', '<div class="alert alert-warning" role="alert"><strong>Disclaimer</strong> This software is <strong>for research purposes only</strong>.</span></div>');
       }
     }
 

src/SessionList.ts

@@ -73,10 +73,10 @@ abstract class ASessionList {
     });
     $enter.select('a[data-action="select"]').on('click', (d) => {
       stopEvent();
-      if (!canWrite(d)) {
-        manager.cloneLocal(d);
-      } else {
+      if (canWrite(d)) {
         manager.loadGraph(d);
+      } else {
+        manager.cloneLocal(d);
       }
       return false;
     });
@@ -308,11 +308,19 @@ export class PersistentSessionList extends ASessionList {
         {
           const $tr = $parent.select('#session_others tbody').selectAll('tr').data(otherworkspaces);
 
-          const $trEnter = $tr.enter().append('tr').html(`
-              <td></td>
-              <td></td>
-              <td></td>
-              <td>${ASessionList.createButton('clone')}</td>`);
+          const $trEnter = $tr.enter().append('tr').html((d) => {
+            let actions = '';
+            if(canWrite(d)) {
+              actions += ASessionList.createButton('select');
+            }
+            actions += ASessionList.createButton('clone');
+
+            return `
+            <td></td>
+            <td></td>
+            <td></td>
+            <td>${actions}</td>`;
+          });
 
           this.registerActionListener(manager, $trEnter);
           $tr.select('td').text((d) => d.name);
@@ -345,11 +353,19 @@ export class PersistentSessionList extends ASessionList {
         {
           const $tr = $parent.select('#session_others').selectAll('div').data(otherworkspaces);
 
-          const $trEnter = $tr.enter().append('div').classed('sessionEntry', true).html(`
+          const $trEnter = $tr.enter().append('div').classed('sessionEntry', true).html((d) => {
+            let actions = '';
+            if(canWrite(d)) {
+              actions += ASessionList.createButton('select');
+            }
+            actions += ASessionList.createButton('clone');
+
+            return `
               <span></span>
               <span></span>
               <span></span>
-              <span>${ASessionList.createButton('clone')}</span>`);
+              <span>${actions}</span>`;
+          });
 
           this.registerActionListener(manager, $trEnter);
           $tr.select('span').text((d) => d.name);

src/dialogs.ts

@@ -10,11 +10,11 @@ export {setGlobalErrorTemplate} from 'phovea_ui/src/errors';
 export {errorAlert as showErrorModalDialog} from './notifications';
 
 export interface IDialogModule {
-  generateDialog(title: string, primaryBtnText?: string): Dialog;
+  generateDialog(title: string, primaryBtnText?: string, additionalCSSClasses?: string): Dialog;
 
   areyousure(msg?: string, options?: IAreYouSureOptions | string): Promise<boolean>;
 
-  FormDialog: {new(title: string, primaryBtnText?: string, formId?: string): FormDialog};
+  FormDialog: {new(title: string, primaryBtnText?: string, formId?: string, additionalCSSClasses?: string): FormDialog};
 }
 
 export function lazyDialogModule(): Promise<IDialogModule> {
@@ -26,9 +26,9 @@ export function lazyDialogModule(): Promise<IDialogModule> {
  * @param {CLUEGraphManager} manager
  * @param {string} id session id
  */
-export function showProveanceGraphNotFoundDialog(manager: CLUEGraphManager, id: string) {
+export function showProveanceGraphNotFoundDialog(manager: CLUEGraphManager, id: string, additionalCSSClasses: string = '') {
   lazyDialogModule().then(({generateDialog}) => {
-    const dialog = generateDialog('Session Not Found!', 'Create New Temporary Session');
+    const dialog = generateDialog('Session Not Found!', 'Create New Temporary Session', additionalCSSClasses);
     // append bg-danger to the dialog parent element
     dialog.body.parentElement.parentElement.parentElement.classList.add('bg-danger');
     dialog.body.innerHTML = `

src/extensions.ts

@@ -164,7 +164,7 @@ export interface IViewGroupExtensionDesc extends IPluginDesc {
 
 
 export interface ISelection {
-  readonly idtype: IDType;
+  readonly idtype: IDType; // see phovea_core/src/idtype/manager#resolve
   readonly range: Range;
 
   /**
@@ -175,7 +175,7 @@ export interface ISelection {
 
 export interface IViewContext {
   readonly graph: ProvenanceGraph;
-  readonly desc: IViewPluginDesc;
+  readonly desc: IViewPluginDesc; // see tdp_core/src/views/interfaces#toViewPluginDesc and phovea_core/src/plugin#get
   readonly ref: IObjectRef<any>;
 }
 

src/lineup/ARankingView.ts

@@ -57,16 +57,79 @@ export interface IARankingViewOptions {
    * @default true
    */
   enableOverviewMode: boolean | 'active';
+
   /**
    * enable zoom button
    * @default true
    */
   enableZoom: boolean;
 
+  /**
+   * enable download data button
+   * @default true
+   */
+  enableDownload: boolean;
+
+  /**
+   * enable save list of entities button
+   * @default true
+   */
+  enableSaveRanking: boolean;
+
+  /**
+   * enable collapsing button of side panel
+   * @default true
+   */
+  enableSidePanelCollapsing: boolean;
+
+  /**
+   * enable side panel
+   * @default 'collapsed'
+   */
   enableSidePanel: boolean | 'collapsed' | 'top';
 
+  /**
+   * enable add columns button
+   * @default true
+   */
   enableAddingColumns: boolean;
 
+  /**
+   * enable support columns in the add column dialog
+   * @default true
+   */
+  enableAddingSupportColumns: boolean;
+
+  /**
+   * enable combining columns in the add column dialog
+   * @default true
+   */
+  enableAddingCombiningColumns: boolean;
+
+  /**
+   * enable score columns in the add column dialog
+   * @default true
+   */
+  enableAddingScoreColumns: boolean;
+
+  /**
+   * enable previously created columns in the add column dialog
+   * @default true
+   */
+  enableAddingPreviousColumns: boolean;
+
+  /**
+   * enable database columns in the add column dialog
+   * @default true
+   */
+  enableAddingDatabaseColumns: boolean;
+
+  /**
+   * enable meta data score columns in the add column dialog
+   * @default true
+   */
+  enableAddingMetaDataColumns: boolean;
+
   enableHeaderSummary: boolean;
 
   enableHeaderRotation: boolean;
@@ -91,6 +154,7 @@ export interface IARankingViewOptions {
 
 /**
  * base class for views based on LineUp
+ * There is also AEmbeddedRanking to display simple rankings with LineUp.
  */
 export abstract class ARankingView extends AView {
 
@@ -142,8 +206,17 @@ export abstract class ARankingView extends AView {
     subType: {key: '', value: ''},
     enableOverviewMode: true,
     enableZoom: true,
+    enableDownload: true,
+    enableSaveRanking: true,
     enableAddingColumns: true,
     enableAddingColumnGrouping: false,
+    enableAddingSupportColumns: true,
+    enableAddingCombiningColumns: true,
+    enableAddingScoreColumns: true,
+    enableAddingPreviousColumns: true,
+    enableAddingDatabaseColumns: true,
+    enableAddingMetaDataColumns: true,
+    enableSidePanelCollapsing: true,
     enableSidePanel: 'collapsed',
     enableHeaderSummary: true,
     enableStripedBackground: false,
@@ -158,6 +231,17 @@ export abstract class ARankingView extends AView {
 
   private readonly selectionAdapter: ISelectionAdapter | null;
 
+  /**
+   * Creates a RankingView with the given selection.
+   * Can be wrapped with a ViewWrapper.
+   *
+   * @remarks You need to call init() to actually display the Ranking View.
+   *
+   * @param context with provenance graph to store the executed operations
+   * @param selection The Ids and IdType of the selection
+   * @param parent where to put the ranking view
+   * @param options to configure the ranking view
+   */
   constructor(context: IViewContext, selection: ISelection, parent: HTMLElement, options: Partial<IARankingViewOptions> = {}) {
     super(context, selection, parent);
 
@@ -247,6 +331,10 @@ export abstract class ARankingView extends AView {
     this.selectionAdapter = this.createSelectionAdapter();
   }
 
+  /**
+   * @param params Seperate element that displays the "Showing x of y ..." message
+   * @param onParameterChange eventlistener for content changes
+   */
   init(params: HTMLElement, onParameterChange: (name: string, value: any, previousValue: any) => Promise<any>) {
     return super.init(params, onParameterChange).then(() => {
       // inject stats

src/lineup/internal/LineUpPanelActions.ts

@@ -137,7 +137,7 @@ export default class LineUpPanelActions extends EventHandler {
       <div class="lu-adder">${this.search ? '<button class="fa fa-plus" title="Add Column"></button>' : ''}
       </div>`);
 
-    if (!this.isTopMode) { // top mode doesn't need collapse feature
+    if (!this.isTopMode && this.options.enableSidePanelCollapsing) { // top mode doesn't need collapse feature
       this.node.insertAdjacentHTML('afterbegin', `<a href="#" title="(Un)Collapse"></a>`);
       this.node.querySelector('a')!.addEventListener('click', (evt) => {
         evt.preventDefault();
@@ -148,8 +148,12 @@ export default class LineUpPanelActions extends EventHandler {
 
     const buttons = this.node.querySelector('section');
     this.appendExtraButtons().forEach((b) => buttons.appendChild(b));
-    buttons.appendChild(this.appendSaveRanking());
-    buttons.appendChild(this.appendDownload());
+    if(this.options.enableSaveRanking) {
+      buttons.appendChild(this.appendSaveRanking());
+    }
+    if(this.options.enableDownload) {
+      buttons.appendChild(this.appendDownload());
+    }
     if (this.options.enableZoom) {
       buttons.appendChild(this.createMarkup('Zoom In', 'fa fa-search-plus gap', () => this.fire(LineUpPanelActions.EVENT_ZOOM_IN)));
       buttons.appendChild(this.createMarkup('Zoom Out', 'fa fa-search-minus', () => this.fire(LineUpPanelActions.EVENT_ZOOM_OUT)));
@@ -330,11 +334,13 @@ export default class LineUpPanelActions extends EventHandler {
     }
     const {metaDataOptions, loadedScorePlugins} = await this.resolveScores(this.idType);
 
-    const items: (ISearchOption | IGroupSearchItem<ISearchOption>)[] = [
-      this.groupedDialog('Database Columns', this.getColumnDescription(descs, false))
-    ];
+    const items: (ISearchOption | IGroupSearchItem<ISearchOption>)[] = [];
 
-    if (loadedScorePlugins.length > 0) {
+    if(this.options.enableAddingDatabaseColumns) {
+      items.push(this.groupedDialog('Database Columns', this.getColumnDescription(descs, false)));
+    }
+
+    if (this.options.enableAddingScoreColumns && loadedScorePlugins.length > 0) {
       items.push({
         text: 'Parameterized Scores',
         children: loadedScorePlugins.map((score) => {
@@ -353,36 +359,49 @@ export default class LineUpPanelActions extends EventHandler {
       });
     }
 
-    const scoreDescs = this.getColumnDescription(descs, true);
-    if (scoreDescs.length > 0) {
-      items.push({
-        text: 'Previously Added Columns',
-        children: scoreDescs
-      });
+    if(this.options.enableAddingPreviousColumns) {
+      const scoreDescs = this.getColumnDescription(descs, true);
+      if (scoreDescs.length > 0) {
+        items.push({
+          text: 'Previously Added Columns',
+          children: scoreDescs
+        });
+      }
     }
 
-    const combiningColumns = this.groupedDialog('Combining Columns', [
-      { text: 'Weighted Sum', id: 'weightedSum', action: () => this.addColumn(createStackDesc('Weighted Sum')) },
-      { text: 'Scripted Combination', id: 'scriptedCombination', action: () => this.addColumn(createScriptDesc('Scripted Combination')) },
-      { text: 'Nested', id: 'nested', action: () => this.addColumn(createNestedDesc('Nested')) },
-      { text: 'Min/Max/Mean Combination', id: 'reduce', action: () => this.addColumn(createReduceDesc()) },
-      { text: 'Imposition', id: 'imposition', action: () => this.addColumn(createImpositionDesc()) }
-    ]);
+    const specialColumnsOption = {
+      text: 'Special Columns',
+      children: []
+    };
+
+    if(this.options.enableAddingCombiningColumns) {
+      const combiningColumns = this.groupedDialog('Combining Columns', [
+        { text: 'Weighted Sum', id: 'weightedSum', action: () => this.addColumn(createStackDesc('Weighted Sum')) },
+        { text: 'Scripted Combination', id: 'scriptedCombination', action: () => this.addColumn(createScriptDesc('Scripted Combination')) },
+        { text: 'Nested', id: 'nested', action: () => this.addColumn(createNestedDesc('Nested')) },
+        { text: 'Min/Max/Mean Combination', id: 'reduce', action: () => this.addColumn(createReduceDesc()) },
+        { text: 'Imposition', id: 'imposition', action: () => this.addColumn(createImpositionDesc()) }
+      ]);
+      specialColumnsOption.children.push(combiningColumns);
+    }
 
-    const supportColumns = this.groupedDialog('Support Columns', [
+    if(this.options.enableAddingSupportColumns) {
+      const supportColumns = this.groupedDialog('Support Columns', [
         {text: 'Group Information', id: 'group', action: () => this.addColumn(createGroupDesc('Group'))},
         {text: 'Selection Checkbox', id: 'selection', action: () => this.addColumn(createSelectionDesc())},
         {text: 'Aggregate Group', id: 'aggregate', action: () => this.addColumn(createAggregateDesc())}
-    ]);
+      ]);
+      specialColumnsOption.children.push(supportColumns);
+    }
 
-    items.push({
-      text: 'Special Columns',
-      children: [
-        combiningColumns,
-        supportColumns,
-        ...metaDataOptions
-      ]
-    });
+    if(this.options.enableAddingMetaDataColumns) {
+      specialColumnsOption.children.push(...metaDataOptions);
+    }
+
+    // Only add special columns option if there are any items available
+    if(specialColumnsOption.children.length > 0) {
+      items.push(specialColumnsOption);
+    }
 
     this.search.data = items;
   }