Merge branch 'develop'

.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

@@ -6,6 +6,7 @@ node_modules
 web_modules
 private
 web_modules
+iva-*.tar.gz
 
 # General
 *.jar

cypress.json

@@ -2,5 +2,12 @@
   "baseUrl": "http://localhost:3000/src/",
   "chromeWebSecurity": false,
   "viewportWidth": 1600,
-  "viewportHeight": 660
+  "viewportHeight": 660,
+  "reporter": "mochawesome",
+  "reporterOptions": {
+      "overwrite": false,
+      "html": false,
+      "json": true
+  }
+
 }

cypress/credentials.bat

@@ -0,0 +1,61 @@
+@echo off
+    setlocal enableextensions disabledelayedexpansion
+
+rem set the username using a plain prompt
+	SET /p CYPRESS_username=Enter your Opencga Username [ENTER]:
+rem Call the subroutine to get the password
+    call :getPassword CYPRESS_password
+rem set the study using a plain prompt
+	SET /p CYPRESS_study=Enter the FQN of the Study you want to test (leave empty for default) [ENTER]:
+
+rem Echo what the function returns
+    if defined CYPRESS_password (
+        SET CYPRESS_password=%CYPRESS_password%
+		rem it launches whatever is passed to the script as param
+		%*
+    ) else (
+        echo Password must be defined
+    )
+
+rem End of the process
+    endlocal
+    exit /b
+
+
+rem Subroutine to get the password
+:getPassword returnVar
+    setlocal enableextensions disabledelayedexpansion
+    set "_password="
+
+    rem We need a backspace to handle character removal
+    for /f %%a in ('"prompt;$H&for %%b in (0) do rem"') do set "BS=%%a"
+
+    rem Prompt the user
+    set /p "=Enter your Opencga Password [ENTER]: " <nul
+
+:keyLoop
+    rem retrieve a keypress
+    set "key="
+    for /f "delims=" %%a in ('xcopy /l /w "%~f0" "%~f0" 2^>nul') do if not defined key set "key=%%a"
+    set "key=%key:~-1%"
+
+    rem handle the keypress
+    rem     if No keypress (enter), then exit
+    rem     if backspace, remove character from password and console
+    rem     else add character to password and go ask for next one
+    if defined key (
+        if "%key%"=="%BS%" (
+            if defined _password (
+                set "_password=%_password:~0,-1%"
+                setlocal enabledelayedexpansion & set /p "=!BS! !BS!"<nul & endlocal
+            )
+        ) else (
+            set "_password=%_password%%key%"
+            set /p "=*"<nul
+        )
+        goto :keyLoop
+    )
+    echo(
+    rem return password to caller
+    if defined _password ( set "exitCode=0" ) else ( set "exitCode=1" )
+    endlocal & set "%~1=%_password%" & exit /b %exitCode%

cypress/credentials.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+echo -n "Enter your Opencga Username [ENTER]: "
+read username
+stty -echo
+printf "Enter your Opencga Password [ENTER]: "
+read password
+stty echo
+echo -en "\nEnter the FQN of the Study you want to test (leave empty for default) [ENTER]: "
+read study
+
+# echo $study > CYPRESS_study
+#"re-opencgahadoop@100k_genomes_grch37_germline:RD37"
+#"re-opencgahadoop@100k_genomes_grch38_germline:RD38"
+#"re-opencgahadoop@100k_genomes_grch38_germline:CG38"
+#"re-opencgahadoop@100k_genomes_grch38_somatic:CS38"
+#study=re-opencgahadoop@100k_genomes_grch38_somatic:CS38
+
+CYPRESS_username=$username CYPRESS_password=$password CYPRESS_study=$study "$@"