Merge branch 'master' into addDefaultExplorer

lib/role.js

@@ -34,26 +34,31 @@ function lookupRole (uri) {
   if (!uri.term && uri.indexOf(igemPrefix) === 0) {
     return {
       uri: uri,
-      term: uri.slice(igemPrefix.length)
+      term: uri.slice(igemPrefix.length),
+      description: { name: uri.slice(igemPrefix.length) }
     }
   }
 
   if (!uri.term && uri.lastIndexOf('#') >= 0 && uri.lastIndexOf('#') + 1 < uri.length) {
     return {
       uri: uri,
-      term: uri.slice(uri.lastIndexOf('#') + 1)
+      term: uri.slice(uri.lastIndexOf('#') + 1),
+      description: { name: uri.slice(uri.lastIndexOf('#') + 1) }
     }
   }
 
   if (!uri.term && uri.lastIndexOf('/') >= 0 && uri.lastIndexOf('/') + 1 < uri.length) {
     return {
       uri: uri,
-      term: uri.slice(uri.lastIndexOf('/') + 1)
+      term: uri.slice(uri.lastIndexOf('/') + 1),
+      description: { name: uri.slice(uri.lastIndexOf('/') + 1) }
     }
   }
 
   return {
-    uri: uri
+    uri: uri,
+    term: uri,
+    description: { name: uri }
   }
 }
 

lib/type.js

@@ -21,13 +21,15 @@ function lookupType (uri) {
       return {
         uri: uri,
         term: soTerm,
-        description: sequenceOntology[soTerm]
+        description: sequenceOntology[soTerm] ? sequenceOntology[soTerm] : { name: soTerm }
       }
     }
   }
 
   return {
-    uri: uri
+    uri: uri,
+    term: uri,
+    description: uri
   }
 }
 

lib/views/admin/status.js

@@ -12,6 +12,7 @@ module.exports = function (req, res) {
     osRelease: os.release(),
     nodeVersion: process.version,
     instanceName: config.get('instanceName'),
+    frontendUrl: config.get('frontendURL'),
     instanceUrl: config.get('instanceUrl'),
     listenPort: config.get('port'),
     sparqlEndpoint: config.get('triplestore').sparqlEndpoint,

lib/views/admin/theme.js

@@ -36,8 +36,12 @@ function form (req, res) {
 
   var locals = {
     instanceName: config.get('instanceName'),
+    frontendURL: config.get('frontendURL'),
+    instanceUrl: config.get('instanceUrl'),
+    uriPrefix: config.get('databasePrefix'),
     frontPageText: config.get('frontPageText'),
     firstLaunch: config.get('firstLaunch'),
+    altHome: config.get('altHome'),
     currentTheme: currentTheme,
     themeParameters: themeParameters
   }
@@ -71,7 +75,7 @@ function post (req, res) {
           if (!newParameter.startsWith('#')) {
             newParameter = '#' + newParameter
           }
-          var pat = /#[123456789abcdef]{6}/i
+          var pat = /#[0123456789abcdef]{6}/i
           if (newParameter.length === 7 && pat.test(newParameter)) {
             console.log('match=' + newParameter)
             newParameters[parameter.variable] = newParameter
@@ -109,6 +113,13 @@ function post (req, res) {
     publishUpdate = true
   }
 
+  console.log(typeof (req.body))
+
+  if (typeof req.body === 'object' && 'altHome' in req.body && req.body.altHome !== config.get('altHome')) {
+    config.set('altHome', req.body.altHome)
+    publishUpdate = true
+  }
+
   if (publishUpdate) {
     updateWor()
   }

lib/views/setup.js

@@ -19,8 +19,10 @@ const settingsSchema = Joi.object({
   userName: requiredString('Please enter a username for the initial user account'),
   userFullName: requiredString('Please enter a full name for the initial user account'),
   userEmail: requiredString('Please enter a valid e-mail address for the initial user account').email(),
-  instanceUrl: requiredString('Please enter the URL of your instance'),
+  frontendURL: Joi.string().allow(''),
+  instanceUrl: requiredString('Please enter the backend URL of your instance'),
   uriPrefix: requiredString('Please enter the URI prefix of your instance'),
+  altHome: Joi.string().allow(''),
   frontPageText: requiredString('Please enter some welcome text for your homepage'),
   userPassword: requiredString('Please enter a password for the initial user account', { trim: false }),
   userPasswordConfirm: requiredString("Passwords didn't match", { trim: false }).valid(Joi.ref('userPassword')),
@@ -54,8 +56,10 @@ module.exports = function (req, res) {
 
   const settings = {
     instanceName: 'My SynBioHub',
+    frontendURL: '',
     instanceUrl: req.protocol + '://' + req.get('Host') + '/',
     uriPrefix: req.protocol + '://' + req.get('Host') + '/',
+    altHome: '',
     userName: '',
     affiliation: '',
     userFullName: '',
@@ -91,8 +95,10 @@ async function setupPost (req, res, settings) {
     {
       ...settings,
       instanceName: req.body.instanceName,
-      instanceUrl: req.body.instanceURL,
+      frontendURL: req.body.frontendURL || '',
+      instanceUrl: req.body.instanceUrl,
       uriPrefix: req.body.uriPrefix,
+      altHome: req.body.altHome || '',
       userName: req.body.userName,
       affiliation: req.body.affiliation,
       userFullName: req.body.userFullName,
@@ -112,14 +118,24 @@ async function setupPost (req, res, settings) {
     { abortEarly: false }
   )
 
-  if (updatedSettings.instanceUrl[updatedSettings.instanceUrl.length - 1] !== '/') {
+  console.log(updatedSettings)
+
+  if (updatedSettings.frontendURL && updatedSettings.frontendURL[updatedSettings.frontendURL.length - 1] !== '/') {
+    updatedSettings.frontendURL += '/'
+  }
+
+  if (updatedSettings.instanceUrl && updatedSettings.instanceUrl[updatedSettings.instanceUrl.length - 1] !== '/') {
     updatedSettings.instanceUrl += '/'
   }
 
   if (updatedSettings.uriPrefix[updatedSettings.uriPrefix.length - 1] !== '/') {
     updatedSettings.uriPrefix += '/'
   }
 
+  if (updatedSettings.altHome && updatedSettings.altHome[updatedSettings.altHome.length - 1] !== '/') {
+    updatedSettings.altHome += '/'
+  }
+
   if (error) {
     if (req.accepts('text/html')) {
       return setupForm(req, res, updatedSettings, {
@@ -140,13 +156,14 @@ async function setupPost (req, res, settings) {
   config.set('sessionSecret', uuid())
   config.set('shareLinkSalt', uuid())
   config.set('passwordSalt', uuid())
+  config.set('frontendURL', updatedSettings.frontendURL)
   config.set('instanceUrl', updatedSettings.instanceUrl)
   config.set('webOfRegistries', { [updatedSettings.uriPrefix.slice(0, -1)]: updatedSettings.instanceUrl.slice(0, -1) })
-  config.set('databasePrefix', updatedSettings.instanceUrl)
   config.set('themeParameters', { default: { baseColor: updatedSettings.color } })
   config.set('frontPageText', updatedSettings.frontPageText)
   config.set('allowPublicSignup', updatedSettings.allowPublicSignup)
   config.set('databasePrefix', updatedSettings.uriPrefix)
+  config.set('altHome', updatedSettings.altHome)
 
   config.set('triplestore', {
     ...config.get('triplestore'),

templates/views/setup.jade

@@ -51,11 +51,11 @@ block body
             h2 2. Some technical details
             div.form-group
                 p
-                    | We need to know where this SynBioHub instance is hosted so we can assign URLs to your submissions.  The instance URL has been automatically guessed as
+                    | Backend Url: We need to know where this SynBioHub instance is hosted so we can assign URLs to your submissions.  The instance URL has been automatically guessed as
                     b  #{settings.instanceUrl}
                     |, but if this is incorrect, please change it here.
                 label Instance URL
-                    input.form-control(name='instanceURL',value=settings.instanceUrl)
+                    input.form-control(name='instanceUrl',value=settings.instanceUrl)
                 p
                     | We need to know how to prefix URIs of objects stored in this SynBioHub. Its default is the same as the URL, and should only be changed if you are shadowing another instance.
                 label URI Prefix   

tests/first_time_setup.py

@@ -26,7 +26,7 @@ def test_post(self):
             'userPassword': 'test',
             'userPasswordConfirm': 'test',
             'instanceName': 'Test Synbiohub',
-            'instanceURL': 'http://localhost:7777/',
+            'instanceUrl': 'http://localhost:7777/',
             'uriPrefix': 'http://localhost:7777/',
             'color': '#D25627',
             'frontPageText': 'text',