Adding unit tests for clinvar export Vue app (#692)

Closes: #692
Related-Issue: #692
Projected-Results-Impact: none

.github/workflows/ci.yml

@@ -82,6 +82,12 @@ jobs:
           coverage report
       - name: check formatting
         run: make black arg=--check
+      - name: Codecov
+        run: |
+          curl -s https://uploader.codecov.io/latest/linux/codecov > /tmp/codecov
+          chmod +x /tmp/codecov
+          /tmp/codecov -cF python
+          /tmp/codecov -cF javascript
       - name: Coveralls
         uses: AndreMiras/coveralls-python-action@develop
         with:
@@ -98,6 +104,12 @@ jobs:
       - name: Run linting
         run: flake8
         if: ${{ matrix.python-version == '3.8' }}
+      - name: Run Vue app tests
+        run: make test_clinvar_export_vue
+        if: ${{ matrix.python-version == '3.8' }}
+      - name: Lint Vue app
+        run: make lint_clinvar_export_vue
+        if: ${{ matrix.python-version == '3.8' }}
 
   coveralls_finish:
     needs: build

HISTORY.rst

@@ -127,6 +127,7 @@ Full Change List
 - Fixing issue with phenotype name in Clinvar (#689).
 - Initial vue.js implementation for small variant filtration (#563).
 - Changing ClinVar link-out to VCV entry instead of coordinates (#693).
+- Adding unit test for clinvar Vue app (#692).
 
 ------
 v1.2.0

Makefile

@@ -63,6 +63,15 @@ test: collectstatic
 test-noselenium:
 	VARFISH_KIOSK_MODE=0 SKIP_SELENIUM=1 coverage run manage.py test -v2 --settings=config.settings.test
 
+
+.PHONY: test_clinvar_export_vue
+test_clinvar_export_vue:
+	npm run --prefix varfish/vueapp test:unit $(arg)
+
+.PHONY: lint_clinvar_export_vue
+lint_clinvar_export_vue:
+	npm run --prefix varfish/vueapp lint $(arg)
+
 .PHONY: lint
 lint: flake8
 

docker/Dockerfile

@@ -62,7 +62,7 @@ RUN ["/bin/bash","-c", "cd /tmp && \
         rm -f Miniconda3-latest-Linux-x86_64.sh"]
 
 # Install modern nodejs
-RUN curl -sL https://deb.nodesource.com/setup_12.x | bash - && \
+RUN curl -sL https://deb.nodesource.com/setup_14.x | bash - && \
     apt install nodejs
 
 # Install npm dependencies.

utility/install_os_gitlab.sh

@@ -32,5 +32,5 @@ apt-get -y install libldap2-dev
 echo "***********************************************"
 echo "Installing Node.js"
 echo "***********************************************"
-curl -sL https://deb.nodesource.com/setup_12.x | bash -
+curl -sL https://deb.nodesource.com/setup_14.x | bash -
 apt-get install -y nodejs

utility/install_vue_dev.sh

@@ -2,8 +2,8 @@
 echo "***********************************************"
 echo "Installing Node.js"
 echo "***********************************************"
-curl -sL https://deb.nodesource.com/setup_12.x | sudo -E bash -
-sudo apt-get install -y nodejs npm
+curl -sL https://deb.nodesource.com/setup_14.x | sudo -E bash -
+sudo apt-get install -y nodejs
 
 echo "***********************************************"
 echo "Installing Vue CLI and Init"

varfish/vueapp/.editorconfig

@@ -1,5 +1,9 @@
 [*.{js,jsx,ts,tsx,vue}]
+line_length = 120
 indent_style = space
 indent_size = 2
 trim_trailing_whitespace = true
 insert_final_newline = true
+
+[*.html]
+line_length = 120

varfish/vueapp/.eslintrc.js

@@ -0,0 +1,24 @@
+module.exports = {
+  plugins: ['simple-import-sort'],
+  rules: {
+    'comma-dangle': 0,
+    'simple-import-sort/imports': 'error',
+    'simple-import-sort/exports': 'error',
+  },
+  extends: ['plugin:vue/recommended', '@vue/standard', 'prettier'],
+  root: true,
+  env: {
+    node: true,
+  },
+  parserOptions: {
+    parser: '@babel/eslint-parser',
+  },
+  overrides: [
+    {
+      files: ['**/tests/unit/**/*.spec.js'],
+      env: {
+        jest: true,
+      },
+    },
+  ],
+}

varfish/vueapp/.prettierignore

@@ -0,0 +1,4 @@
+/dist/
+/coverage/
+/webpack-stats.json
+.nyc_output

varfish/vueapp/README.md

@@ -1,29 +1,35 @@
 # vueapp
 
 ## Project setup
+
 ```
 npm install
 ```
 
 ### Compiles and hot-reloads for development
+
 ```
 npm run serve
 ```
 
 ### Compiles and minifies for production
+
 ```
 npm run build
 ```
 
 ### Run your unit tests
+
 ```
 npm run test:unit
 ```
 
 ### Lints and fixes files
+
 ```
 npm run lint
 ```
 
 ### Customize configuration
+
 See [Configuration Reference](https://cli.vuejs.org/config/).

varfish/vueapp/babel.config.js

@@ -1,5 +1,3 @@
 module.exports = {
-  presets: [
-    '@vue/cli-plugin-babel/preset'
-  ]
+  presets: ['@vue/cli-plugin-babel/preset'],
 }

varfish/vueapp/jest.config.js

@@ -0,0 +1,18 @@
+module.exports = {
+  collectCoverage: true,
+  collectCoverageFrom: [
+    'src/**/*.{js,vue}',
+    '!**/index.js',
+    '!src/constants.js',
+    '!src/main.js',
+  ],
+  moduleNameMapper: {
+    '^@/(.*)$': '<rootDir>/src/$1',
+  },
+  moduleFileExtensions: ['js', 'json', 'vue'],
+  transform: {
+    '^.+\\.js$': 'babel-jest',
+    '^.+\\.vue$': '@vue/vue2-jest',
+  },
+  preset: '@vue/cli-plugin-unit-jest',
+}