Merge pull request #199 from Caleydo/release_v5.0.0

Release v5.0.0

.circleci/config.yml

@@ -3,13 +3,11 @@ jobs:
   build:
     working_directory: ~/phovea
     docker:
-      - image: circleci/node:6-browsers
-    tags:
-      - /v\d+.\d+.\d+.*/
+      - image: circleci/node:8-browsers
     steps:
       - checkout
       - restore_cache:
-          key: deps2-{{ .Branch }}-{{ checksum "package.json" }}
+          key: deps1-{{ checksum "package.json" }}
       - run:
           name: install-npm-wee
           command: npm install
@@ -18,7 +16,7 @@ jobs:
           command: |
             (grep -l '._resolved.: .\(git[^:]*\|bitbucket\):' ./node_modules/*/package.json || true) | xargs -r dirname | xargs -r rm -rf
       - save_cache:
-          key: deps2-{{ .Branch }}-{{ checksum "package.json" }}
+          key: deps1-{{ checksum "package.json" }}
           paths:
           - ./node_modules
       - run: #install all dependencies
@@ -29,3 +27,20 @@ jobs:
           command: npm run dist
       - store_artifacts:
           path: dist
+
+workflows:
+  version: 2
+  build-branch:
+    jobs:
+      - build:
+          filters:
+            tags:
+              ignore: /^v.*/
+  build-tag:
+    jobs:
+      - build:
+          filters:
+            branches:
+              ignore: /.*/
+            tags:
+              only: /^v.*/

.travis.yml

@@ -1,14 +1,13 @@
 language: node_js
 
 node_js:
-- 6
+- 8
 
 addons:
   firefox: 49.0.1
 
 before_install:
 - export DISPLAY=:99.0
 - sh -e /etc/init.d/xvfb start
-- if [[ `npm -v` != 3* ]]; then npm i -g npm@3; fi
 
-script: npm run dist
+script: npm run dist

.yo-rc.json

@@ -25,7 +25,14 @@
       "node_modules.*(d3|bootstrap|jquery|select2)",
       "((node_modules.*popper)|lineupjs|lineupengine|tdp_core)"
     ],
-    "extensions": [],
+    "extensions": [
+      {
+        "type": "ordinoWelcomeView",
+        "id": "ordinoWelcomeView",
+        "module": "WelcomeView",
+        "extras": {}
+      }
+    ],
     "sextensions": [],
     "libraries": [
       "scrollTo",

package.json

@@ -2,7 +2,7 @@
   "name": "ordino",
   "description": "Target discovery platform for exploring rankings of genes, disease models, and other entities.",
   "homepage": "https://phovea.caleydo.org",
-  "version": "4.0.1",
+  "version": "5.0.0",
   "author": {
     "name": "The Caleydo Team",
     "email": "[email protected]",
@@ -29,7 +29,7 @@
     "predocker": "npm run build",
     "docker": "docker build -t ordino -f deploy/Dockerfile .",
     "compile": "tsc",
-    "lint": "tslint -c tslint.json src/**.ts tests/**.ts",
+    "lint": "tslint -c tslint.json -p .",
     "docs": "typedoc --options typedoc.json src/**.ts",
     "prebuild": "node -e \"process.exit(process.env.PHOVEA_SKIP_TESTS === undefined?1:0)\" || npm run test",
     "pretest": "npm run compile",
@@ -47,47 +47,47 @@
     "dist": "mkdirp dist && cd build && tar cvzf ../dist/ordino.tar.gz *"
   },
   "devDependencies": {
-    "@types/jasmine": "2.5.41",
-    "awesome-typescript-loader": "3.0.3",
-    "cache-loader": "1.2.0",
-    "css-loader": "0.26.1",
-    "extract-text-webpack-plugin": "2.0.0-rc.3",
+    "@types/jasmine": "2.5.47",
+    "awesome-typescript-loader": "3.1.2",
+    "css-loader": "0.28.0",
     "extract-loader": "0.1.0",
-    "file-loader": "0.10.0",
-    "fork-ts-checker-webpack-plugin": "0.2.9",
-    "html-loader": "0.4.4",
-    "imports-loader": "0.7.0",
+    "extract-text-webpack-plugin": "2.1.0",
+    "file-loader": "0.11.1",
+    "html-loader": "0.4.5",
+    "imports-loader": "0.7.1",
     "jasmine": "2.5.3",
     "json-loader": "0.5.4",
-    "karma": "1.4.0",
+    "karma": "1.5.0",
     "karma-chrome-launcher": "2.0.0",
-    "karma-firefox-launcher": "1.0.0",
+    "karma-firefox-launcher": "1.0.1",
     "karma-jasmine": "1.1.0",
     "karma-junit-reporter": "2.0.0",
     "karma-sourcemap-loader": "0.3.7",
-    "karma-webpack": "2.0.2",
+    "karma-webpack": "2.0.3",
     "mkdirp": "0.5.1",
-    "node-sass": "4.5.0",
+    "node-sass": "4.7.2",
     "null-loader": "0.1.1",
     "raw-loader": "0.5.1",
-    "sass-loader": "5.0.0",
-    "style-loader": "0.13.1",
-    "thread-loader": "1.1.2",
-    "ts-loader": "3.1.1",
-    "tslib": "1.5.0",
-    "tslint": "4.4.2",
-    "typedoc": "0.5.5",
-    "typescript": "2.2.0",
-    "url-loader": "0.5.7",
-    "webpack": "2.2.1",
+    "sass-loader": "6.0.7",
+    "style-loader": "0.16.1",
+    "tslib": "1.9.0",
+    "tslint": "5.9.1",
+    "typedoc": "0.11.1",
+    "typescript": "2.7.2",
+    "url-loader": "0.5.8",
+    "webpack": "2.3.3",
     "webpack-dev-server": "2.4.2",
-    "ifdef-loader": "2.0.0"
+    "cache-loader": "1.2.0",
+    "ifdef-loader": "2.0.0",
+    "fork-ts-checker-webpack-plugin": "0.4.1",
+    "thread-loader": "1.1.2",
+    "ts-loader": "4.0.1"
   },
   "dependencies": {
     "@types/jquery.scrollto": "1.4.27",
     "jquery.scrollto": "2.1.2",
     "@types/jquery": "2.0.33",
     "jquery": "3.1.1",
-    "tdp_core": "github:datavisyn/tdp_core#v4.0.1"
+    "tdp_core": "github:datavisyn/tdp_core#semver:^5.0.0"
   }
 }

phovea.js

@@ -60,6 +60,9 @@ module.exports = function (registry) {
     priority: 95
   });
 
+  registry.push('ordinoWelcomeView', 'ordinoWelcomeView', function() { return import('./src/WelcomeView'); }, {
+    priority: 10
+  });
   // generator-phovea:end
 };
 

src/WelcomeView.ts

@@ -0,0 +1,16 @@
+import WelcomeViewTemplate from 'html-loader!./welcome_view.html';
+
+export interface IWelcomeView {
+  build();
+}
+
+export default class WelcomeView implements IWelcomeView {
+
+  constructor(private parent: HTMLElement) {
+    //
+  }
+
+  build() {
+    this.parent.innerHTML = WelcomeViewTemplate;
+  }
+}

src/index.ts

@@ -16,4 +16,4 @@ import './style.scss';
 
 import Ordino from './Ordino';
 
-new Ordino();
+const _ = new Ordino();

src/internal/OrdinoApp.ts

@@ -19,8 +19,10 @@ import {createView, removeView, replaceView, setAndUpdateSelection, setSelection
 import Range from 'phovea_core/src/range/Range';
 import {SESSION_KEY_NEW_ENTRY_POINT} from './constants';
 import * as session from 'phovea_core/src/session';
+import {list as listPlugins} from 'phovea_core/src/plugin';
+import {IWelcomeView} from '../WelcomeView';
 
-import WelcomeViewTemplate from 'html-loader!../welcome_view.html';
+export const EXTENSION_POINT_WELCOME_PAGE = 'ordinoWelcomeView';
 
 
 /**
@@ -62,7 +64,29 @@ export default class OrdinoApp extends EventHandler {
 
     const $wrapper = d3.select(parent).append('div').classed('wrapper', true);
     this.$node = $wrapper.append('div').classed('targid', true).datum(this);
-    this.$node.html(WelcomeViewTemplate);
+    this.buildWelcomeView(<HTMLElement>this.$node.node());
+  }
+
+  /**
+   * Loads registered welcome pages from the extension points.
+   * The welcome page with the highest priority is loaded and shown.
+   *
+   * @param {HTMLElement} parent
+   */
+  private buildWelcomeView(parent: HTMLElement) {
+    const welcomeViews = listPlugins(EXTENSION_POINT_WELCOME_PAGE)
+      .sort((a: any, b: any) => ((b.priority || 10) - (a.priority || 10))); // descending
+
+    if(welcomeViews.length === 0) {
+      console.warn('No registered welcome page found!');
+      return;
+    }
+
+    welcomeViews[0].load()
+      .then((p) => {
+        const welcomeView: IWelcomeView = p.factory(parent);
+        welcomeView.build();
+      });
   }
 
   private buildHistory(parent: HTMLElement) {

src/internal/ViewWrapper.ts

@@ -26,13 +26,13 @@ import {
   isSameSelection,
   IView,
   IViewContext,
-  IViewPluginDesc,
   matchLength,
   showAsSmallMultiple,
   toViewPluginDesc
 } from 'tdp_core/src/views';
 import {resolveImmediately} from 'phovea_core/src/internal/promise';
 import {groupByCategory} from 'tdp_core/src/views/findViews';
+import {MODE_ANIMATION_TIME} from './constants';
 
 function generate_hash(desc: IPluginDesc, selection: ISelection) {
   const s = (selection.idtype ? selection.idtype.id : '') + 'r' + (selection.range.toString());
@@ -97,11 +97,12 @@ export default class ViewWrapper extends EventHandler {
    * Initialize this view, create the root node and the (inner) view
    * @param graph
    * @param selection
+   * @param itemSelection
    * @param parent
    * @param plugin
    * @param options
    */
-  constructor(private readonly graph: ProvenanceGraph, public selection: ISelection, parent: Element, private plugin: IPlugin, public options?) {
+  constructor(private readonly graph: ProvenanceGraph, public selection: ISelection, itemSelection: ISelection|null, parent: Element, private plugin: IPlugin, private firstTime: boolean, public options?) {
     super();
 
     // create provenance reference
@@ -112,7 +113,7 @@ export default class ViewWrapper extends EventHandler {
     // create ViewWrapper root node
     this.$viewWrapper = d3.select(parent).append('div').classed('viewWrapper', true);
 
-    this.built = resolveImmediately(this.createView(selection, plugin, options));
+    this.built = resolveImmediately(this.createView(selection, itemSelection, plugin, options));
   }
 
   /**
@@ -136,7 +137,7 @@ export default class ViewWrapper extends EventHandler {
    * @param plugin
    * @param options
    */
-  private createView(selection: ISelection, plugin: IPlugin, options?) {
+  private createView(selection: ISelection, itemSelection: ISelection|null, plugin: IPlugin, options?) {
     this.$node = this.$viewWrapper.append('div')
       .classed('view', true)
       .datum(this);
@@ -164,6 +165,10 @@ export default class ViewWrapper extends EventHandler {
 
     this.instance = plugin.factory(this.context, selection, <Element>$inner.node(), options, plugin.desc);
     return resolveImmediately(this.instance.init(<HTMLElement>$params.node(), this.onParameterChange.bind(this))).then(() => {
+      if (itemSelection) {
+        return this.instance.setItemSelection(itemSelection);
+      }
+    }).then(() => {
       this.instance.on(AView.EVENT_ITEM_SELECT, this.listenerItemSelect);
       this.instance.on(AView.EVENT_UPDATE_ENTRY_POINT, this.listenerUpdateEntryPoint);
 
@@ -178,15 +183,16 @@ export default class ViewWrapper extends EventHandler {
    * @param plugin
    * @param options
    */
-  replaceView(selection: ISelection, plugin: IPlugin, options?) {
+  replaceView(selection: ISelection, itemSelection: ISelection|null, plugin: IPlugin, firstTime: boolean, options?) {
     this.destroyView();
 
     this.selection = selection;
     this.plugin = plugin;
     this.options = options;
+    this.firstTime = firstTime;
 
     this.init(this.graph, selection, plugin, options);
-    return this.built = this.createView(selection, plugin, options);
+    return this.built = this.createView(selection, itemSelection, plugin, options);
   }
 
   /**
@@ -216,7 +222,15 @@ export default class ViewWrapper extends EventHandler {
   }
 
 
-  private onParameterChange(name: string, value: any, previousValue: any) {
+  private onParameterChange(name: string, value: any, previousValue: any, isInitializion: boolean) {
+    if (isInitializion) {
+      if (this.firstTime) {
+        return this.context.graph.pushWithResult(setParameter(this.ref, name, value, previousValue), {
+          inverse: setParameter(this.ref, name, previousValue, value)
+        });
+      }
+      return; // dummy;
+    }
     return this.context.graph.push(setParameter(this.ref, name, value, previousValue));
   }
 
@@ -282,12 +296,25 @@ export default class ViewWrapper extends EventHandler {
     // trigger modeChanged
     this.instance.modeChanged(mode);
 
+    this.updateAfterAnimation();
+
     // on focus view scroll into view
     if (mode === EViewMode.FOCUS) {
       this.scrollIntoView();
     }
   }
 
+  private updateAfterAnimation() {
+    if (!this.instance || typeof (<any>this.instance).update !== 'function') {
+      return;
+    }
+    setTimeout(() => {
+      if ((<any>this.instance) && typeof (<any>this.instance).update === 'function') {
+        (<any>this.instance).update();
+      }
+    }, MODE_ANIMATION_TIME);
+  }
+
   private scrollIntoView() {
     const prev = (<any>this.$viewWrapper.node()).previousSibling;
     const scrollToPos = prev ? prev.offsetLeft || 0 : 0;
@@ -371,10 +398,10 @@ export default class ViewWrapper extends EventHandler {
   }
 }
 
-export function createViewWrapper(graph: ProvenanceGraph, selection: ISelection, parent: Element, plugin: IPluginDesc, options?) {
-  return plugin.load().then((p) => new ViewWrapper(graph, selection, parent, p, options));
+export function createViewWrapper(graph: ProvenanceGraph, selection: ISelection, itemSelection: ISelection|null, parent: Element, plugin: IPluginDesc, firstTime: boolean, options?) {
+  return plugin.load().then((p) => new ViewWrapper(graph, selection, itemSelection, parent, p, firstTime, options));
 }
 
-export function replaceViewWrapper(existingView: ViewWrapper, selection: ISelection, plugin: IPluginDesc, options?) {
-  return plugin.load().then((p) => existingView.replaceView(selection, p, options));
+export function replaceViewWrapper(existingView: ViewWrapper, selection: ISelection, itemSelection: ISelection|null, plugin: IPluginDesc, firstTime: boolean, options?) {
+  return plugin.load().then((p) => existingView.replaceView(selection, itemSelection, p, firstTime, options));
 }