.gitbook.yaml

@@ -0,0 +1,3 @@
+
+root: ./docs/
+

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,31 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/docker.yml

@@ -0,0 +1,57 @@
+name: CI
+
+on:
+  push:
+    branches-ignore:
+      - '**'
+    #branches: [ develop ]
+
+jobs:
+  build:
+    name: Install deps and Build
+    runs-on: ubuntu-18.04
+    steps:
+      ## Install deps and build IVA
+      - uses: actions/checkout@v2
+      - name: IVA Npm install and Prepare
+        run: |
+          npm install bower
+          npm install && npm run prepare
+      - name: Jsorolla Npm install
+        run: |
+          git submodule update --init
+          cd lib/jsorolla
+          npm install bower
+          npm install
+      - name: Npm build
+        run: npm run build
+      - name: LS
+        run: ls
+      - name: Upload webpack artifact
+        uses: actions/upload-artifact@v2
+        with:
+          name: webpack-artifact
+          path: build
+          retention-days: 1
+
+  deploy:
+    name: Publish Docker image in DockerHub repository
+    runs-on: ubuntu-18.04
+    needs: build
+    steps:
+      ## Publish docker image to DockerHub
+      - uses: actions/checkout@v2
+      - name: Download webpack artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: webpack-artifact
+          path: build
+      - name: Read package.json
+        uses: "tyankatsu0105/read-package-version-actions@v1"
+        id: package-version
+      - name: Show version number
+        run: echo "Version is ${{ steps.package-version.outputs.version }}"
+      - name: Login to dockerhub
+        run: echo "${{ secrets.DOCKER_HUB_PASSWORD }}" | docker login --username ${{ secrets.DOCKER_HUB_USER }} --password-stdin
+      - name: Build and Publish Docker image
+        run: python3 ./docker/docker-build.py push --images app --tag ${{ steps.package-version.outputs.version }}

.github/workflows/release.yml

@@ -0,0 +1,43 @@
+name: "release"
+
+on:
+  push:
+    branches-ignore:
+      - '**'
+    #branches: [ master ]
+
+jobs:
+  build:
+    name: App build
+    runs-on: ubuntu-18.04
+    steps:
+      ## Install deps and build IVA
+      - uses: actions/checkout@v2
+      - name: IVA Npm install and Prepare
+        run: |
+          npm install bower
+          npm install && npm run prepare
+      - name: Jsorolla Npm install
+        run: |
+          git submodule update --init
+          cd lib/jsorolla
+          npm install bower
+          npm install
+      - name: Npm build
+        run: npm run build
+      - name: Read package.json
+        uses: "tyankatsu0105/read-package-version-actions@v1"
+        id: package-version
+      - name: Show version number
+        run: |
+          echo "Version is ${{ steps.package-version.outputs.version }}"
+      - name: Create release
+        uses: "marvinpinto/action-automatic-releases@latest"
+        with:
+          repo_token: "${{ secrets.GITHUB_TOKEN }}"
+          draft: true
+          automatic_release_tag: "v${{ steps.package-version.outputs.version }}"
+          title: "v${{ steps.package-version.outputs.version }}"
+          prerelease: false
+          files: |
+            iva-${{ steps.package-version.outputs.version }}.tar.gz

.gitignore

@@ -1,8 +1,12 @@
 
 build
+dist
 bower_components
 node_modules
+web_modules
 private
+web_modules
+iva-*.tar.gz
 
 # General
 *.jar

Jenkinsfile

@@ -1,28 +1,48 @@
 pipeline {
     agent any
     stages {
-         stage ('Build') {
+        stage ('Build source code') {
             options {
                 timeout(time: 5, unit: 'MINUTES')
             }
             steps {
-                sh 'cd lib/jsorolla && npm install && cd ../.. && npm install --unsafe-perm && npm run build'
+                sh 'npm install --unsafe-perm && npm run build'
             }
         }
-	stage ('Docker Build and Push') {
+	    stage ('Build and Push Stable Docker') {
             options {
                 timeout(time: 25, unit: 'MINUTES')
             }
- 		steps {
-	        script {
-                        def tag = sh(returnStdout: true, script: "git tag --sort version:refname | tail -1").trim()	       
-		        sh "docker build  -t opencb/iva:'${tag}' -f docker/Dockerfile ."
-                        withDockerRegistry([ credentialsId: "wasim-docker-hub", url: "" ]) {
-	       			sh "docker push opencb/iva:'${tag}'"
-			}	              
-		}		
+            when {
+                branch "master"
+            }
+ 		    steps {
+	            script {
+                    def tag = sh(returnStdout: true, script: "node -p \"require('./package.json').version\"").trim()
+		            sh "docker build  -t opencb/iva:'${tag}' -f docker/Dockerfile ."
+                    withDockerRegistry([ credentialsId: "wasim-docker-hub", url: "" ]) {
+	       			    sh "docker push opencb/iva:'${tag}'"
+			        }
+		        }
            }
-       }
-  }
+        }
+        stage ('Build and Push Development Docker') {
+            options {
+                timeout(time: 25, unit: 'MINUTES')
+            }
+            when {
+                branch "develop"
+            }
+        	steps {
+       	        script {
+                    def tag = sh(returnStdout: true, script: "node -p \"require('./package.json').version\"").trim()
+       		        sh "docker build  -t opencb/iva:'${tag}' -f docker/Dockerfile ."
+                    withDockerRegistry([ credentialsId: "wasim-docker-hub", url: "" ]) {
+       	       		    sh "docker push opencb/iva:'${tag}'"
+       			    }
+       		    }
+            }
+        }
+    }
 }
 

README.md

@@ -1,5 +1,8 @@
+<img src="src/img/iva_logo.png" alt="Logo"/>
+
 # Overview
-IVA is a generic Interactive Variant Analysis browser that can be used for the visualization of biological information from various data sources. IVA uses data from [OpenCGA](https://github.com/opencb/opencga) which is an OpenCB project.
+
+The Interactive Variant Analyser (IVA) is the web user interface for OpenCGA that provides unprecedented features for real-time interaction with genomic data. It is suitable for any scale; from the detailed interpretation of a single genomic test through to assessing the genetic diversity of hundreds of thousands of aggregated genomes. It is not just for bioinformaticians; it provides simple and convenient access for biomedical researchers and clinical scientists as well.
 
 ### Documentation
 You can find IVA documentation and tutorials at: https://github.com/opencb/iva/wiki.
@@ -18,6 +21,7 @@ IVA is versioned following the rules from [Semantic versioning](http://semver.or
 ### Maintainers
 We recommend to contact IVA developers by writing to OpenCB mailing list opencb@googlegroups.com. The main developers and maintainers are:
 * Ignacio Medina (im411@cam.ac.uk) (_Founder and Project Leader_)
+* Antonio Altamura (antonio.altamura@genomicsengland.co.uk)
 * Javier Perez Florido (javier.perez.florido.ext@juntadeandalucia.es)
 * Alexis Martínez (alexis.martinez@juntadeandalucia.es)
 
@@ -29,18 +33,16 @@ We recommend to contact IVA developers by writing to OpenCB mailing list opencb@
 IVA is an open-source and collaborative project, currently developement is mainly carried out by Stefan Gräf and Ignacio Medina teams from the University of Cambridge and Joaquin Dopazo team from CIBERER. We appreciate any help and feedback from users, you can contribute in many different ways such as simple bug reporting and feature request. Dependending on your skills you are more than welcome to develop client tools, new features or even fixing bugs.
 
 # How to build
-IVA is developed in HTML5, therefore it is mainly developed in JavaScript and makes a heavy usage of HTML and CSS. It uses Grunt as building tool. IVA also requires of OpenCB JSorolla project to be built, this is a JavaScript library developed for several OpenCB web-based projects, this can be found as Git submodule in IVA.
+IVA is mainly developed in JavaScript. It requires of OpenCB JSorolla project to be built, this is a JavaScript library developed for several OpenCB web-based projects, it can be found as Git submodule in IVA.
 
-Stable releases are merged and tagged at _master_ branch, you are encourage to use latest stable release for production. Current active development is carried out at _develop_ branch, only building is guaranteed and bugs are expected, use this branch for development or for testing new functionalities. The only dependency of IVA from OpenCB is JSorolla.
+Stable releases are merged and tagged at _master_ branch, you are encourage to use latest stable release for production. Current active development is carried out at _develop_ branch, only building is guaranteed and bugs are expected, use this branch for development or for testing new functionalities.
 
 ### Prerequisites
-The following technologies are needed to build IVA: [Node.js](https://nodejs.org/en/), [npm](https://www.npmjs.com/) and [Grunt](http://gruntjs.com/getting-started).
+To run and build IVA you need: [Node.js](https://nodejs.org/en/) and [npm](https://www.npmjs.com/).
 
 ##### Installing Node.js and npm
 To install [Node.js](https://nodejs.org/en/) you can visit [this link](http://blog.teamtreehouse.com/install-node-js-npm-linux).
 
-[npm](https://www.npmjs.com/) stands for *node packaged modules* and it is the dependency manager of [Node.js](https://nodejs.org/en/).
-
 ### Cloning
 IVA is an open-source project and can be downloaded either as package(tar.gz) from GitHub releases or source code by cloning the repository.
 
@@ -49,11 +51,12 @@ Default ***develop*** branch can be downloaded by executing:
 ```
 $ git clone https://github.com/opencb/iva.git
 Cloning into 'iva'...
-remote: Counting objects: 624, done.
-remote: Total 624 (delta 0), reused 0 (delta 0), pack-reused 624
-Receiving objects: 100% (624/624), 139.37 KiB | 0 bytes/s, done.
-Resolving deltas: 100% (356/356), done.
-Checking connectivity... done.
+remote: Enumerating objects: 126, done.
+remote: Counting objects: 100% (126/126), done.
+remote: Compressing objects: 100% (72/72), done.
+remote: Total 10370 (delta 70), reused 85 (delta 38), pack-reused 10244
+Receiving objects: 100% (10370/10370), 4.70 MiB | 61.00 KiB/s, done.
+Resolving deltas: 100% (6064/6064), done.
 ```
 
 Latest stable release at ***master*** branch can be downloaded by executing:
@@ -69,53 +72,53 @@ Checking connectivity... done.
 ```
 
 After this, in both cases, you **must** execute the following command to fetch the JSorolla submodule (only the first time):
- 
+
 ```
 git submodule update --init
 ```
 
-Go to lib/jsorolla and checkout to ***develop*** branch of Jsorolla by 
+Go to `./lib/jsorolla` and checkout to ***develop*** branch of Jsorolla by
 
 ```
 cd lib/jsorolla
 git checkout develop
+npm run install
 ```
 
-### Build
-First, you must update JSorolla dependencies, from the root folder execute:
+### Run
+To run IVA in dev mode (hot reload for CSS files and hot restart (aka live reloading) for JS scripts), run
 
-```
-cd lib/jsorolla
-npm install
-```
+`
+npm run serve
+`.
 
-Finally, to build IVA execute:
+### Build
+To buil IVA, just run
+
+`
+npm run build
+`.
 
-We have to install npm packages for IVA, from the the root folder execute:
+### Test
+We use [Cypress.io](https://www.cypress.io/) as testing framework.
 
+Having the project running through the command `npm run serve`, you can run the interactive E2E test suite by running the command
 ```
-npm install
+npm run e2e
 ```
 
-And now execute:
-
+#### Run tests and generate a report
+To run test in headless version (no browser) and generate a report, run
 ```
-npm run build
+npm run e2e-report
 ```
+for more help, try ```npm run e2e-report -h```.
 
-when completed, all compiled files will be located under the _build_ folder.
-
-### Testing
-You can copy build content to a web server such as Apache HTTP Server and open your favourite internet browser to open IVA.
-
-### Execute Tests in development with nightwatch(http://nightwatchjs.org/)
-Prerequisite: make sure you have JDK installed, with at least version 8. If you don't have it, you can grab it from http://www.oracle.com/technetwork/java/javase/downloads/index.html.
-
-1. npm install --dev
-2. Selenium server. Download the latest release .jar from http://selenium-release.storage.googleapis.com/index.html. i.e. selenium-server-standalone-3.7.0.jar
-3. Chromedriver. Download from https://sites.google.com/a/chromium.org/chromedriver/downloads that version which supports your chrome versión. You can review what version fits your browser here https://chromedriver.storage.googleapis.com/2.33/notes.txt.
-4. Create a bin folder inside your test folder in root path
-5. Move selenium bin and chrome bin inside that bin folder.
-6. npm run test-e2e ( or ./node_modules/.bin/nightwatch test/e2e/clinical-prioritization.js if you want execute just one)
-
+For Windows environment, just add the suffix `-win`
+```
+npm run e2e-win
+npm run e2e-report-win
+```
+for more help, try ```npm run e2e-report-win -h```.
 
+The HTML report will be generated in `./report`. The filename will have the structure `<OPENCGA_STUDY_FQN>__<TIME>_<DATE>.html`