Merge pull request #266 from DoctorBud/modernize2

Update deps. Use BioLink API

.eslintrc.js

@@ -0,0 +1,35 @@
+const errorInProduction = process.env.NODE_ENV === 'production' ? 'error' : 'off';
+const path = require('path');
+
+module.exports = {
+  root: true,
+  env: {
+    node: true,
+    browser: true
+  },
+  extends: [
+  ],
+  rules: {
+    'no-console': 0, // errorInProduction,
+    'no-debugger': errorInProduction,
+    'brace-style': 0,
+    // 'brace-style': [2, 'stroustrup'],
+    'padded-blocks': 0,
+    // 'indent': [2, 2, { 'SwitchCase': 1 }],
+    'indent': 0,
+    'spaced-comment': 0,
+    'quotes': 0,
+    // 'quotes': ['error', 'single', { 'allowTemplateLiterals': true }],
+    'global-require': 0,
+    'no-unused-vars': [0, { 'argsIgnorePattern': '^_' }],
+    'quote-props': [0],
+    'prefer-destructuring': 0,
+    'prefer-arrow-callback': 0,
+    'prefer-template': 0,
+    'comma-dangle': 0,
+    'max-len': 0,
+    'no-param-reassign': 0,
+    'no-underscore-dangle': 0,
+  },
+};
+

.gitignore

@@ -1,11 +1,12 @@
 ## Ignore npm libs.
 node_modules
+dist
 
 ## Ignore python behave tests generated libs
 tests/behave/lib
 tests/behave/bin
 tests/behave/lib64
-tests/behave/include 
+tests/behave/include
 tests/behave/ghostdriver.log
 
 ## Others

.npmignore

@@ -1,11 +1,12 @@
 .travis.yml
 
 .jshintrc
+.eslintrc.js
 
 .gitignore
 
 tests/behave/lib
 tests/behave/bin
 tests/behave/lib64
-tests/behave/include 
+tests/behave/include
 tests/behave/ghostdriver.log

.travis.yml

@@ -2,23 +2,39 @@ sudo: required
 
 language: node_js
 
+env:
+  - MOZ_HEADLESS=1
+addons:
+  firefox: latest
+
 node_js:
-  - "0.12"
+  - "v8.12.0"
 
 before_install:
-  - "sudo pip install --upgrade pip"
-  - "sudo pip install selenium"
-  - "sudo pip install behave"
-
+  - wget https://github.com/mozilla/geckodriver/releases/download/v0.23.0/geckodriver-v0.23.0-linux64.tar.gz
+  - mkdir geckodriver
+  - tar -xzf geckodriver-v0.23.0-linux64.tar.gz -C geckodriver
+  - export PATH=$PATH:$PWD/geckodriver
+  - "cd tests/behave"
+  - "virtualenv env"
+  - "source env/bin/activate"
+  - "pip install selenium"
+  - "pip install --ignore-installed behave"
+  - "cd ../.."
+  # - "sudo pip install --upgrade pip"
+  # - "sudo pip install selenium"
+  # - "sudo pip install --ignore-installed behave"
+
 install:
   - "npm install"
 
-script: 
-  - "gulp bundle"
-  - "gulp test"
+script:
+  - "npx gulp bundle"
+  - "npx gulp test"
   - "PGDIR=`pwd`"
   - "cd tests/behave"
-  - "TARGET=file://$PGDIR BROWSER=phantomjs behave"
+  - "source env/bin/activate"
+  - "TARGET=file://$PGDIR DRAFT=6 behave"
 
 # whitelist
 branches:

README.md

@@ -6,7 +6,7 @@
 
 ## About Phenogrid
 
-Phenogrid is a Javascript component that visualizes semantic similarity calculations provided by [OWLSim](https://github.com/owlcollab/owltools), as provided through APIs from the [Monarch Initiative](http://monarchinitiative.org/).
+Phenogrid is a Javascript component that visualizes semantic similarity calculations provided by [OWLSim](https://github.com/owlcollab/owltools), as provided through APIs from the [Monarch Initiative](https://monarchinitiative.org/).
 
 Given an input list of phenotypes (you will see the sample input below) and parameters specified in config/phenogrid_config.js indicating desired source of matching models (humans, model organisms, etc.), the phenogrid will call the Monarch API to get OWLSim results and render them in your web browser in data visualization. And you may use the visualized data for your research.
 
@@ -281,7 +281,7 @@ var data = {
 window.onload = function() {
     // There are three species that are loaded and each of them has simsearch matches.
     Phenogrid.createPhenogridForElement(document.getElementById('phenogrid_container'), {
-        serverURL : "http://monarchinitiative.org",
+        serverURL : "https://monarchinitiative.org",
         gridSkeletonData: data
     });
 }
@@ -303,7 +303,7 @@ window.onload = function() {
 
 This URL should be pointed to the OWLSim URL server associated with your installation containing the Monarch web services. You have three options:
 - Use http://beta.monarchinitiative.org to connect to the development/test web services. This server is less stable than the production server.
-- Use http://monarchinitiative.org to connect to the stable, production version of the web services (better uptime)
+- Use https://monarchinitiative.org to connect to the stable, production version of the web services (better uptime)
 - If you are running the complete monarch-app, you can point it to http://localhost:8080, or whichever server/port you are using in your local installation.
 
 

config/phenogrid_config.js

@@ -1,6 +1,5 @@
 var configoptions = {
-    serverURL: "https://beta.monarchinitiative.org",
+    serverURL: "https://monarchinitiative.org",
     selectedCalculation: 0,
     selectedSort: "Frequency"
 };
-