MAINT: Read-only user

Refactor measurements

.gitignore

@@ -15,4 +15,4 @@
 /libpeerconnection.log
 npm-debug.log
 testem.log
-.divshot-cache
+.firebase

app/adapters/application.js

@@ -1,9 +1,13 @@
 import DS from 'ember-data';
 import DataAdapterMixin from 'ember-simple-auth/mixins/data-adapter-mixin';
+import Ember from 'ember';
 
+const { inject: { service } } = Ember;
 const { RESTAdapter } = DS;
 
 export default RESTAdapter.extend(DataAdapterMixin, {
+  globals: service(),
+
   authorizer: 'authorizer:application',
 
   namespace: function() {

app/adapters/user.js

@@ -0,0 +1,7 @@
+import ApplicationAdapter from '../adapters/application';
+
+export default ApplicationAdapter.extend({
+  // If coalesceFindRequests is on, and we 403 on any requests, ESA logs
+  // the current user out. Better to split the requests up at the adapter level.
+  coalesceFindRequests: false,
+});

app/authenticators/oauth2.js

@@ -1,6 +1,70 @@
 import OAuth2PasswordGrant from 'ember-simple-auth/authenticators/oauth2-password-grant';
 import config from '../config/environment';
+import parseBase64 from '../utils/parse-base64';
+import Ember from 'ember';
+const { RSVP: { Promise }, isEmpty, run, Logger: { warn } } = Ember;
 
 export default OAuth2PasswordGrant.extend({
   serverTokenEndpoint: `${config.apiURL}/api/authenticate`,
+  serverTokenRefreshEndpoint: `${config.apiURL}/api/refresh`,
+
+  authenticate: function(identification, password) {
+    return new Promise((resolve, reject) => {
+      const data = { username: identification, password };
+      const serverTokenEndpoint = this.get('serverTokenEndpoint');
+      this.makeRequest(serverTokenEndpoint, data).then((response) => {
+        run(() => {
+          const token = parseBase64(response['access_token']);
+          const expiresAt = this._absolutizeExpirationTime(token['exp']);
+          this._scheduleAccessTokenRefresh(expiresAt, response['access_token']);
+          if (!isEmpty(expiresAt)) {
+            response = Ember.merge(response, { 'expires_at': expiresAt });
+          }
+          resolve(response);
+        });
+      }, (xhr) => {
+        run(null, reject, xhr.responseJSON || xhr.responseText);
+      });
+    });
+  },
+
+  _scheduleAccessTokenRefresh: function(expiresAt, accessToken) {
+    if (this.get('refreshAccessTokens')) {
+      const now = (new Date()).getTime();
+      const offset = (Math.floor(Math.random() * 5) + 5) * 1000;
+      if (!isEmpty(accessToken) && !isEmpty(expiresAt) && expiresAt > now - offset) {
+        run.cancel(this._refreshTokenTimeout);
+        delete this._refreshTokenTimeout;
+        if (!Ember.testing) {
+          this._refreshTokenTimeout = run.later(this, this._refreshAccessToken, expiresAt, accessToken, expiresAt - now - offset);
+        }
+      }
+    }
+  },
+
+  _refreshAccessToken: function(expiresAt, accessToken) {
+    const data = { 'token': accessToken };
+    const serverTokenRefreshEndpoint = this.get('serverTokenRefreshEndpoint');
+    return new Promise((resolve, reject) => {
+      this.makeRequest(serverTokenRefreshEndpoint, data).then((response) => {
+        run(() => {
+          const token = parseBase64(response['access_token']);
+          const expiresAt = this._absolutizeExpirationTime(token['exp']);
+          const data = Ember.merge(response, { 'expires_at': expiresAt });
+          this._scheduleAccessTokenRefresh(expiresAt, response['access_token']);
+          this.trigger('sessionDataUpdated', data);
+          resolve(data);
+        });
+      }, (xhr, status, error) => {
+        warn(`Access token could not be refreshed - server responded with ${error}.`);
+        reject();
+      });
+    });
+  },
+
+  _absolutizeExpirationTime: function(expiresAt) {
+    if (!isEmpty(expiresAt)) {
+      return new Date(expiresAt * 1000).getTime();
+    }
+  }
 });

app/helpers/get-property.js

@@ -2,7 +2,6 @@ import Ember from 'ember';
 
 const { get, Helper: { helper } } = Ember;
 
-// This will be unneccesary when ember 2.0 lands
 export default helper(function(params) {
   return get(params[0], params[1]);
 });

app/initializers/global-variables.js

@@ -1,20 +0,0 @@
-import Ember from 'ember';
-import config from '../config/environment';
-
-var globals = Ember.Object.extend({
-  genus: config.APP.genus,
-  apiURL: config.apiURL,
-});
-
-export function initialize(container, application) {
-  application.register('service:globals', globals, {singleton: true});
-  application.inject('route', 'globals', 'service:globals');
-  application.inject('controller', 'globals', 'service:globals');
-  application.inject('component', 'globals', 'service:globals');
-  application.inject('adapter', 'globals', 'service:globals');
-}
-
-export default {
-  name: 'global-variables',
-  initialize: initialize
-};

app/mirage/config.js

@@ -19,11 +19,13 @@ export function testConfig() {
   this.post('/species');
   this.get('/species/:id');
   this.put('/species/:id');
+  this.delete('/species/:id');
 
   this.get('/characteristics');
   this.post('/characteristics');
   this.get('/characteristics/:id');
   this.put('/characteristics/:id');
+  this.delete('/characteristics/:id');
 
   this.get('/strains', function(db /*, request*/) {
     return {
@@ -39,4 +41,5 @@ export function testConfig() {
     };
   });
   this.put('/strains/:id');
+  this.delete('/strains/:id');
 }

app/mixins/delete-model.js

@@ -8,6 +8,10 @@ export default Mixin.create({
   actions: {
     delete: function() {
       this.get('model').destroyRecord().then(() => {
+        // Instead of unloading the entire store, we keep the loaded user models
+        ['species', 'strain', 'characteristic', 'measurement'].map((model) => {
+          this.get('store').unloadAll(model);
+        });
         this.transitionToRoute(this.get('transitionRoute'));
       });
     },

app/mixins/save-model.js

@@ -23,11 +23,16 @@ export default Mixin.create({
 
     cancel: function() {
       const model = this.get('model');
+      const isNew = model.get('isNew');
 
       model.get('errors').clear();
       model.rollbackAttributes();
 
-      this.transitionToRoute(this.get('fallbackRouteCancel'), model);
+      if (isNew) {
+        this.transitionToRoute(this.get('fallbackRouteCancel'));
+      } else {
+        this.transitionToRoute(this.get('fallbackRouteCancel'), model);
+      }
     },
   },
 });

app/models/species.js

@@ -1,6 +1,5 @@
 import DS from 'ember-data';
 import config from '../config/environment';
-import Ember from 'ember';
 
 const { Model, attr, hasMany } = DS;
 
@@ -17,9 +16,4 @@ export default Model.extend({
   updatedBy   : attr('number'),
   sortOrder   : attr('number'),
   canEdit     : attr('boolean'),
-
-  // TODO: move this to component/helper
-  speciesNameMU: function() {
-    return Ember.String.htmlSafe(`<em>${this.get('speciesName')}</em>`);
-  }.property('speciesName').readOnly(),
 });

app/models/strain.js

@@ -2,6 +2,7 @@ import DS from 'ember-data';
 import Ember from 'ember';
 
 const { Model, hasMany, belongsTo, attr } = DS;
+const { computed, String: { htmlSafe } } = Ember;
 
 export default Model.extend({
   measurements       : hasMany('measurements', { async: false }),
@@ -22,19 +23,8 @@ export default Model.extend({
   sortOrder          : attr('number'),
   canEdit            : attr('boolean'),
 
-  // TODO: move this to component/helper
-  strainNameMU: function() {
-    let type = this.get('typeStrain') ? '<sup>T</sup>' : '';
-    return Ember.String.htmlSafe(`${this.get('strainName')}${type}`);
-  }.property('strainName', 'typeStrain').readOnly(),
-
-  // TODO: move this to component/helper
-  fullName: Ember.computed('species', 'strainName', function() {
-    return `${this.get('species.speciesName')} ${this.get('strainNameMU')}`;
+  fullNameMU: computed('species', 'strainName', function() {
+    const type = this.get('typeStrain') ? '<sup>T</sup>' : '';
+    return htmlSafe(`<em>${this.get('species.speciesName')}</em> ${this.get('strainName')}${type}`);
   }),
-
-  // TODO: move this to component/helper
-  fullNameMU: function() {
-    return Ember.String.htmlSafe(`<em>${this.get('species.speciesName')}</em> ${this.get('strainNameMU')}`);
-  }.property('species', 'strainNameMU').readOnly(),
 });

app/pods/components/delete-button/component.js

@@ -1,13 +1,23 @@
 import Ember from 'ember';
 
-export default Ember.Component.extend({
-  tagName: 'button',
-  classNames: ["button-red", "smaller"],
+const { Component } = Ember;
 
-  click: function() {
-    if (window.confirm("Do you really want to delete this?")) {
+export default Component.extend({
+  tagName: 'span',
+  showConfirmDelete: false,
+
+  actions: {
+    initialClick: function() {
+      this.set('showConfirmDelete', true);
+    },
+
+    cancelDelete: function() {
+      this.set('showConfirmDelete', false);
+    },
+
+    confirmDelete: function() {
       this.attrs.delete();
-    }
+    },
   },
 
 });

app/pods/components/delete-button/template.hbs

@@ -1 +1,12 @@
-Delete
+{{#unless showConfirmDelete}}
+  <button class="button-red smaller delete" {{action "initialClick"}}>
+    Delete
+  </button>
+{{else}}
+  <button class="button-red smaller delete-confirm" {{action "confirmDelete"}}>
+    Confirm Delete
+  </button>
+  <button class="button-gray smaller delete-cancel" {{action "cancelDelete"}}>
+    Cancel Delete
+  </button>
+{{/unless}}

app/pods/components/genus-name/component.js

@@ -1,8 +1,14 @@
 import Ember from 'ember';
 
-export default Ember.Component.extend({
+const { Component, computed, inject: { service } } = Ember;
+
+export default Component.extend({
+  globals: service(),
+
   tagName: 'em',
-  genus: function() {
+
+  genus: computed('globals.genus', function() {
     return this.get('globals.genus').capitalize();
-  }.property().readOnly(),
+  }),
+
 });

app/pods/components/site-logo/component.js

@@ -1,3 +1,7 @@
 import Ember from 'ember';
 
-export default Ember.Component.extend({});
+const { Component, inject: { service } } = Ember;
+
+export default Component.extend({
+  globals: service(),
+});

app/pods/components/strain-name/template.hbs

@@ -0,0 +1 @@
+{{strain.strainName}}{{{if strain.typeStrain '<sup>T</sup>' ''}}}

app/pods/components/text-editor/component.js

@@ -1,13 +1,25 @@
 import Ember from 'ember';
 /* global Quill */
 
-export default Ember.Component.extend({
-  quill: null,
+const { Component } = Ember;
+
+export default Component.extend({
+  // Passed in
   value: null,
-  update: null,
+
+  // Internal
+  quill: null,
+
+  didReceiveAttrs() {
+    this._super(...arguments);
+
+    if (!this.attrs.update) {
+      throw new Error(`You must provide an \`update\` action.`);
+    }
+  },
 
   didInsertElement: function() {
-    let quill = new Quill(`#${this.get('elementId')} .editor`, {
+    const quill = new Quill(`#${this.get('elementId')} .editor`, {
       formats: ['bold', 'italic', 'underline'],
       modules: {
         'toolbar': { container: `#${this.get('elementId')} .toolbar` }

app/pods/components/x-application/component.js

@@ -1,10 +1,12 @@
 import Ember from 'ember';
 
-export default Ember.Component.extend({
+const { Component, inject: { service } } = Ember;
+
+export default Component.extend({
   classNames: ["flakes-frame"],
 
-  session: Ember.inject.service('session'),
-  currentUser: Ember.inject.service('session-account'),
+  session: service(),
+  currentUser: service('session-account'),
 
   didInsertElement: function() {
     FlakesFrame.init();

app/pods/components/x-application/template.hbs

@@ -33,7 +33,7 @@
       <br>
       {{link-to 'Sign Up' 'users.new'}}
       <br>
-      {{link-to 'Locked Out?' 'users.requestlockouthelp'}}
+      {{link-to 'Reset Password' 'users.requestlockouthelp'}}
     </p>
   {{/if}}
 </div>

app/pods/components/x-select/component.js

@@ -1,50 +1,54 @@
 import Ember from 'ember';
 
-const { Component, isEmpty } = Ember;
+const { Component, get, run: { schedule } } = Ember;
 
 export default Component.extend({
   tagName: 'select',
-
-  nameAttr: null,
-  listItems: null,
-  placeholder: null,
-  selected: null,
-  selectize: null,
-  multiple: false,
-
   attributeBindings: [
     'multiple',
   ],
 
+  options: null,
+  selected: null,
+  nameAttr: null,
+  placeholder: null,
+
   change: function() {
-    this.attrs["update"](this.$()[0].selectize.getValue());
-  },
+    let selectedInComponent = this.get('selected');
+    let selectedInWidget = this.$().val();
 
-  didReceiveAttrs: function() {
-    this._super(...arguments);
-    console.log('didReceiveAttrs');
-
-    if (!this.attrs.update) {
-      throw new Error(`You must provide an \`update\` action.`);
+    if (this.get('multiple')) {
+      if (selectedInWidget === null) {
+        selectedInWidget = [];
+      }
+      selectedInComponent = selectedInComponent.toString();
+      selectedInWidget = selectedInWidget.toString();
     }
 
-    Ember.run.schedule('actions', this, () => {
-      console.log('before adding');
-      this.$()[0].selectize.setValue(this.get('selected'), true);
-      console.log('after adding')
-    });
+    // We need this to prevent an infinite loop of afterRender -> change.
+    if (selectedInComponent !== selectedInWidget) {
+      this.attrs.update(this.$().val());
+    }
   },
 
   didInsertElement: function() {
-    console.log('didInsertElement');
-    const options = {
-      closeAfterSelect: true,
-      selectOnTab: true,
-      plugins: ['drag_drop'],
-      items: this.get('selected'),
-    }
+    let options = {};
+    options.placeholder = this.get('placeholder');
+    options.templateResult = function(item) {
+      if (!item.disabled) {
+        const text = get(item, 'element.innerHTML');
+        const $item = Ember.$(`<span>${text}</span>`);
+        return $item;
+      }
+    };
+    this.$().select2(options);
+  },
 
-    this.$().selectize(options);
+  didRender: function() {
+    const selected = this.get('selected');
+    schedule('afterRender', this, function() {
+      this.$().val(selected).trigger('change');
+    });
   },
 
 });

app/pods/components/x-select/template.hbs

@@ -1,6 +1,3 @@
-{{#if placeholder}}
-  <option value="">{{placeholder}}</option>
-{{/if}}
-{{#each listItems as |option|}}
-  <option value={{option.id}} selected={{equal option.id value.id}}>{{get-property option nameAttr}}</option>
+{{#each options as |option|}}
+  <option value={{option.id}}>{{get-property option nameAttr}}</option>
 {{/each}}

app/pods/login/login-form/template.hbs

@@ -10,3 +10,7 @@
 <div>
   {{link-to 'Forget your password?' 'users.requestlockouthelp'}}
 </div>
+<br>
+<div>
+  Just checking things out? Log in with email <code>read-only</code> and password <code>bacteria</code>!
+</div>

app/pods/protected/characteristics/show/characteristic-card/template.hbs

@@ -26,7 +26,6 @@
         <dl class="span-2">
           <dt>Measurements</dt>
           <dd>
-            <p>To add/edit/remove a measurement, please visit the strain's page (links below)</p>
             {{protected/characteristics/show/measurements-table characteristic=characteristic}}
           </dd>
         </dl>

app/pods/protected/characteristics/show/measurements-table/component.js

@@ -1,7 +1,7 @@
 import Ember from 'ember';
 
 const { Component, computed } = Ember;
-const { sort } = computed;
+const { alias, sort } = computed;
 
 export default Component.extend({
   characteristic: null,
@@ -10,10 +10,9 @@ export default Component.extend({
     return this.get('characteristic.measurements.length') > 0;
   }),
 
-  sortParams: ['characteristic.characteristicTypeName', 'characteristic.sortOrder', 'characteristic.characteristicName'],
-  sortAsc: true,
-  paramsChanged: false,
-  sortedMeasurements: sort('characteristic.measurements', 'sortParams'),
+  measurements: alias('characteristic.measurements'),
+  sortParams: ['strain.sortOrder'],
+  sortedMeasurements: sort('measurements', 'sortParams'),
 
   actions: {
     changeSortParam: function(col) {

app/pods/protected/characteristics/show/measurements-table/template.hbs

@@ -7,24 +7,24 @@
 <table class="flakes-table">
   <thead>
     <tr>
-      <th {{action "changeSortParam" "strain.strainName"}} class="click">Strain</th>
+      <th {{action "changeSortParam" "strain.sortOrder"}} class="click">Strain</th>
       <th {{action "changeSortParam" "value"}} class="click">Value</th>
       <th {{action "changeSortParam" "notes"}} class="click">Notes</th>
     </tr>
   </thead>
   <tbody>
-    {{#each sortedMeasurements as |row|}}
+    {{#each sortedMeasurements as |measurement|}}
       <tr>
         <td>
-          {{#link-to 'protected.strains.show' row.strain.id}}
-            {{{row.strain.strainNameMU}}}
+          {{#link-to 'protected.strains.show' measurement.strain.id classBinding="measurement.strain.typeStrain:type-strain"}}
+            {{measurement.strain.fullNameMU}}
           {{/link-to}}
         </td>
         <td>
-          {{row.value}}
+          {{measurement.value}}
         </td>
         <td>
-          {{row.notes}}
+          {{measurement.notes}}
         </td>
       </tr>
     {{/each}}

app/pods/protected/characteristics/show/route.js

@@ -4,7 +4,7 @@ const { Route } = Ember;
 
 export default Route.extend({
   model: function(params) {
-    return this.store.findRecord('characteristic', params.characteristic_id);
+    return this.store.findRecord('characteristic', params.characteristic_id, { reload: true });
   },
 
 });

app/pods/protected/compare/controller.js

@@ -3,8 +3,8 @@ import Ember from 'ember';
 const { Controller } = Ember;
 
 export default Controller.extend({
-  selectedStrains: null,
-  selectedCharacteristics: null,
+  selectedStrains: [],
+  selectedCharacteristics: [],
 
   actions: {
     search: function(query) {
@@ -12,12 +12,10 @@ export default Controller.extend({
     },
 
     updateStrainSelection: function(selection) {
-      console.log(selection);
       this.set('selectedStrains', selection);
     },
 
     updateCharacteristicSelection: function(selection) {
-      console.log(selection);
       this.set('selectedCharacteristics', selection);
     },
   }

app/pods/protected/compare/results/results-table/component.js

@@ -4,6 +4,7 @@ const { Component, computed, inject: { service } } = Ember;
 
 export default Component.extend({
   session: service(),
+  globals: service(),
 
   strains: null,
   characteristics: null,

app/pods/protected/compare/results/results-table/template.hbs

@@ -14,8 +14,16 @@
   <tbody>
     {{#each characteristics as |row|}}
       <tr>
-        {{#each row key="@index" as |col|}}
-          <td>{{col}}</td>
+        {{#each row key="@index" as |col index|}}
+          <td>
+            {{#unless index}}
+              {{#link-to 'protected.characteristics.show' col.id}}
+                {{col.characteristicName}}
+              {{/link-to}}
+            {{else}}
+              {{col}}
+            {{/unless}}
+          </td>
         {{/each}}
       </tr>
     {{/each}}

app/pods/protected/compare/results/route.js

@@ -30,16 +30,15 @@ export default Route.extend({
     }
 
     const compare = this.controllerFor('protected.compare');
-    compare.set('selectedStrains', params.strain_ids.split(','));
-    compare.set('selectedCharacteristics', params.characteristic_ids.split(','));
+    compare.set('selectedStrains', params.strain_ids.split(","));
+    compare.set('selectedCharacteristics', params.characteristic_ids.split(","));
 
     return this.get('ajax').request('/compare', { data: params });
   },
 
   setupController: function(controller, model) {
     model.forEach((m, i) => {
-      const c = this.store.peekRecord('characteristic', m[0]);
-      model[i][0] = c.get('characteristicName');
+      model[i][0] = this.store.peekRecord('characteristic', m[0]);
     });
 
     const compare = this.controllerFor('protected.compare');

app/pods/protected/compare/select-form/component.js

@@ -1,6 +1,6 @@
 import Ember from 'ember';
 
-const { Component } = Ember;
+const { Component, computed: { sort } } = Ember;
 
 export default Component.extend({
   characteristics: null,
@@ -10,12 +10,23 @@ export default Component.extend({
   "update-strains": null,
   "update-characteristics": null,
 
+
+  charSortParams: ['characteristicTypeName', 'sortOrder', 'characteristicName'],
+  sortedCharacteristics: sort('characteristics', 'charSortParams'),
+  strainSortParams: ['sortOrder'],
+  sortedStrains: sort('strains', 'sortParams'),
+
+  selectedStrains: [],
+  selectedCharacteristics: [],
+
   updateStrains: function(selection) {
-    this.attrs["update-strains"](selection);
+    this.set('selectedStrains', selection);
+    this.attrs['update-strains'](this.get('selectedStrains'));
   },
 
   updateCharacteristics: function(selection) {
-    this.attrs['update-characteristics'](selection);
+    this.set('selectedCharacteristics', selection);
+    this.attrs['update-characteristics'](this.get('selectedCharacteristics'));
   },
 
   actions: {
@@ -57,7 +68,7 @@ export default Component.extend({
       this.updateStrains(selection);
     },
 
-    updateCharacteristicSelection: function(selection) {
+    updateCharacteristicsSelection: function(selection) {
       this.updateCharacteristics(selection);
     },
   },

app/pods/protected/compare/select-form/template.hbs

@@ -6,12 +6,12 @@
           <label>Strains</label>
           {{
             x-select
-            listItems=strains
-            nameAttr="fullNameMU"
-            update=(action "updateStrainSelection")
-            placeholder="Select one ore more strains"
+            options=sortedStrains
+            nameAttr='fullNameMU'
             multiple=true
             selected=selectedStrains
+            update=(action "updateStrainSelection")
+            placeholder="Select one or more strains"
           }}
         </li>
         <li>
@@ -26,12 +26,12 @@
           <label>Characteristics</label>
           {{
             x-select
-            listItems=characteristics
-            nameAttr="characteristicName"
-            update=(action "updateCharacteristicSelection")
-            placeholder="Select one ore more characteristics"
+            options=sortedCharacteristics
+            nameAttr='characteristicName'
             multiple=true
             selected=selectedCharacteristics
+            update=(action "updateCharacteristicsSelection")
+            placeholder="Select one or more characteristics"
           }}
         </li>
         <li>

app/pods/protected/species/index/species-table/component.js

@@ -6,7 +6,7 @@ const { Component, computed: { sort } } = Ember;
 export default Component.extend(SetupMetaData, {
   species: null,
 
-  sortParams: ['speciesName', 'strainCount'],
+  sortParams: ['sortOrder'],
   sortedSpecies: sort('species', 'sortParams'),
 
 });

app/pods/protected/species/index/species-table/template.hbs

@@ -23,7 +23,7 @@
           {{#each species.strains as |strain index|}}
             {{if index ","}}
             {{#link-to 'protected.strains.show' strain.id}}
-              {{{strain.strainNameMU}}}
+              {{strain-name strain=strain}}
             {{/link-to}}
           {{/each}}
         </td>

app/pods/protected/species/show/route.js

@@ -4,7 +4,7 @@ const { Route } = Ember;
 
 export default Route.extend({
   model: function(params) {
-    return this.store.findRecord('species', params.species_id);
+    return this.store.findRecord('species', params.species_id, { reload: true });
   },
 
 });

app/pods/protected/species/show/species-card/template.hbs

@@ -14,7 +14,7 @@
               {{#each species.strains as |strain index|}}
                 <li>
                   {{#link-to 'protected.strains.show' strain.id}}
-                    {{{strain.strainNameMU}}}
+                    {{strain-name strain=strain}}
                   {{/link-to}}
                 </li>
               {{/each}}

app/pods/protected/species/species-form/template.hbs

@@ -19,7 +19,7 @@
         {{#each strains as |strain index|}}
           {{if index ","}}
           {{#link-to 'protected.strains.show' strain.id}}
-            {{{strain.strainNameMU}}}
+            {{strain-name strain=strain}}
           {{/link-to}}
         {{/each}}
         {{add-button label="Add Strain" link="protected.strains.new" canAdd=metaData.canAdd}}

app/pods/protected/strains/edit/controller.js

@@ -1,36 +1,61 @@
 import Ember from 'ember';
-import SaveModel from '../../../../mixins/save-model';
-import ajaxError from '../../../../utils/ajax-error';
 
-const { Controller } = Ember;
+const { Controller, RSVP, inject: { service } } = Ember;
+
+export default Controller.extend({
+  ajaxError: service('ajax-error'),
 
-export default Controller.extend(SaveModel, {
-  // Required for SaveModel mixin
   fallbackRouteSave: 'protected.strains.show',
   fallbackRouteCancel: 'protected.strains.show',
 
   actions: {
-    addCharacteristic: function() {
-      return this.store.createRecord('measurement', {
-        characteristic: this.store.createRecord('characteristic', { sortOrder: -999 }),
+    save: function(properties, deleteQueue, updateQueue) {
+      let promises = [];
+      properties.measurements.forEach((measurement) => {
+        if (measurement.get('isNew')) {
+          promises.push(measurement.save());
+        }
+      });
+
+      updateQueue.forEach((measurement) => {
+        promises.push(measurement.save());
+      });
+
+      deleteQueue.forEach((measurement) => {
+        promises.push(measurement.destroyRecord());
+      });
+
+      const model = this.get('model');
+      const fallbackRoute = this.get('fallbackRouteSave');
+
+      RSVP.all(promises).then(() => {
+        // Can't call _super inside promise, have to reproduce save-model
+        // mixin here :-(
+        model.setProperties(properties);
+        model.save().then((model) => {
+          this.get('flashMessages').clearMessages();
+          this.transitionToRoute(fallbackRoute, model);
+        });
+      }, (errors) => {
+        this.get('ajaxError').alert(errors);
       });
     },
 
-    saveMeasurement: function(measurement, properties) {
-      measurement.setProperties(properties);
-      measurement.save().then(() => {
-        this.get('flashMessages').clearMessages();
-      }, () => {
-        ajaxError(measurement.get('errors'), this.get('flashMessages'));
-      });
-    },
+    cancel: function() {
+      const model = this.get('model');
 
-    deleteMeasurement: function(measurement) {
-      const characteristic = measurement.get('characteristic');
-      if (characteristic.get('isNew')) {
-        characteristic.destroyRecord();
+      model.get('errors').clear();
+      model.rollbackAttributes();
+
+      if (model.get('isNew')) {
+        this.transitionToRoute(this.get('fallbackRouteCancel'));
+      } else {
+        this.transitionToRoute(this.get('fallbackRouteCancel'), model);
       }
-      measurement.destroyRecord();
+    },
+
+    addMeasurement: function() {
+      return this.store.createRecord('measurement');
     },
 
   },

app/pods/protected/strains/edit/template.hbs

@@ -2,10 +2,8 @@
   protected/strains/strain-form
   strain=model
   speciesList=speciesList
-  add-characteristic=(action "addCharacteristic")
+  add-measurement=(action "addMeasurement")
   allCharacteristics=allCharacteristics
-  save-measurement=(action "saveMeasurement")
-  delete-measurement=(action "deleteMeasurement")
   on-save=(action "save")
   on-cancel=(action "cancel")
 }}

app/pods/protected/strains/index/strain-table/component.js

@@ -6,7 +6,7 @@ const { Component, computed: { sort } } = Ember;
 export default Component.extend(SetupMetaData, {
   strains: null,
 
-  sortParams: ['fullName'],
+  sortParams: ['sortOrder'],
   sortedStrains: sort('strains', 'sortParams'),
 
 });

app/pods/protected/strains/index/strain-table/template.hbs

@@ -13,7 +13,7 @@
     {{#each sortedStrains as |strain|}}
       <tr>
         <td>
-          {{#link-to 'protected.strains.show' strain classBinding="data.typeStrain:type-strain"}}
+          {{#link-to 'protected.strains.show' strain classBinding="strain.typeStrain:type-strain"}}
             {{strain.fullNameMU}}
           {{/link-to}}
         </td>

app/pods/protected/strains/measurements-table-row/component.js

@@ -10,6 +10,8 @@ export default Component.extend({
   allCharacteristics: null,
   measurement: null,
   isDirty: null,
+  isNew: false,
+  isQueued: false,
 
   // Actions
   "save-measurement": null,
@@ -22,11 +24,23 @@ export default Component.extend({
   notes: null,
 
   resetOnInit: Ember.on('init', function() {
+    this._resetProperties();
+  }),
+
+  _resetProperties: function() {
     this.get('propertiesList').forEach((field) => {
       const valueInMeasurement = this.get('measurement').get(field);
       this.set(field, valueInMeasurement);
     });
-  }),
+    // Read-only attributes
+    this.set('isNew', this.get('measurement.isNew'));
+    if (this.get('isNew') && !this.get('isQueued')) {
+      this.set('isEditing', true);
+    } else {
+      this.set('isEditing', false);
+    }
+    this.set('isDirty', false);
+  },
 
   updateField: function(property, value) {
     this.set(property, value);
@@ -40,12 +54,22 @@ export default Component.extend({
 
   actions: {
     edit: function() {
-      this.toggleProperty('isEditing');
+      this.set('isEditing', true);
     },
 
     save: function() {
       this.attrs['save-measurement'](this.get('measurement'), this.getProperties(this.get('propertiesList')));
-      this.toggleProperty('isEditing');
+      this.set('isQueued', true);
+      this._resetProperties();
+    },
+
+    cancel: function() {
+      if (this.get('isNew')) {
+        this.attrs['delete-measurement'](this.get('measurement'));
+      } else {
+        this._resetProperties();
+        this.set('isEditing', false);
+      }
     },
 
     delete: function() {

app/pods/protected/strains/measurements-table-row/loading/template.hbs

@@ -0,0 +1 @@
+{{loading-panel}}

app/pods/protected/strains/measurements-table-row/template.hbs

@@ -1,5 +1,7 @@
 {{#if isEditing}}
-  <td></td>
+  <td>
+    {{{characteristic.characteristicTypeName}}}
+  </td>
   <td>
     <select onchange={{action "characteristicDidChange" value="target.value"}}>
       {{#each allCharacteristics as |characteristicChoice|}}
@@ -15,14 +17,13 @@
   </td>
   {{#if canEdit}}
     <td>
-      {{#if isDirty}}
-      <button class="button-green smaller" {{action 'save'}}>
-        Save
-      </button>
-      {{else}}
-      <button class="button-gray smaller" {{action 'save'}}>
+      <button class="button-gray smaller" {{action 'cancel'}}>
         Cancel
       </button>
+      {{#if isDirty}}
+        <button class="button-green smaller" {{action 'save'}}>
+          Save
+        </button>
       {{/if}}
     </td>
   {{/if}}

app/pods/protected/strains/measurements-table/component.js

@@ -5,13 +5,13 @@ const { sort } = computed;
 
 export default Component.extend({
   // Passed in
-  strain: null,
+  measurements: null,
   allCharacteristics: null,
   canEdit: false,
   canAdd: false,
 
   // Actions
-  "add-characteristic": null,
+  "add-measurement": null,
   "save-measurement": null,
   "delete-measurement": null,
 
@@ -19,15 +19,11 @@ export default Component.extend({
   sortParams: ['characteristic.characteristicTypeName', 'characteristic.sortOrder', 'characteristic.characteristicName'],
   sortAsc: true,
   paramsChanged: false,
-  sortedMeasurements: sort('strain.measurements', 'sortParams'),
-  measurementsPresent: computed('strain.measurements', function() {
-    return this.get('strain.measurements.length') > 0;
-  }),
+  sortedMeasurements: sort('measurements', 'sortParams'),
 
   actions: {
-    addCharacteristic: function() {
-      const newChar = this.attrs['add-characteristic']();
-      this.get('strain.measurements').addObject(newChar);
+    addMeasurement: function() {
+      return this.attrs['add-measurement']();
     },
 
     changeSortParam: function(col) {

app/pods/protected/strains/measurements-table/template.hbs

@@ -1,17 +1,16 @@
 {{#if canAdd}}
   <br>
-  <button class="button-green smaller" {{action "addCharacteristic"}}>
-    Add characteristic
+  <button class="button-green smaller" {{action "addMeasurement"}}>
+    Add measurement
   </button>
   <br><br>
 {{/if}}
 
-{{#if measurementsPresent}}
-  {{#if paramsChanged}}
-    <button class="button-gray smaller" {{action 'resetSortParam'}}>
-      Reset sort
-    </button>
-  {{/if}}
+{{#if paramsChanged}}
+  <button class="button-gray smaller" {{action 'resetSortParam'}}>
+    Reset sort
+  </button>
+{{/if}}
 <table class="flakes-table">
   <colgroup>
     {{#if canEdit}}
@@ -48,9 +47,10 @@
         allCharacteristics=allCharacteristics
         canEdit=canEdit
       }}
+    {{else}}
+      <tr>
+        <td colspan="5">No Measurements on Record</td>
+      </tr>
     {{/each}}
   </tbody>
 </table>
-{{else}}
-No measurements on record.
-{{/if}}

app/pods/protected/strains/show/route.js

@@ -4,7 +4,7 @@ const { Route } = Ember;
 
 export default Route.extend({
   model: function(params) {
-    return this.store.findRecord('strain', params.strain_id);
+    return this.store.findRecord('strain', params.strain_id, { reload: true });
   },
 
 });

app/pods/protected/strains/show/strain-card/template.hbs

@@ -1,7 +1,7 @@
 <div class="span-1">
   <fieldset class="flakes-information-box">
     <legend>
-      {{strain.strainNameMU}}
+      {{strain-name strain=strain}}
     </legend>
 
     {{! ROW 1 }}
@@ -10,7 +10,7 @@
         <dt>Species</dt>
         <dd>
           {{#link-to 'protected.species.show' strain.species.id}}
-            <em>{{strain.species.speciesNameMU}}</em>
+            <em>{{strain.species.speciesName}}</em>
           {{/link-to}}
         </dd>
       </dl>
@@ -71,11 +71,11 @@
     {{! ROW 5 }}
     <div class="grid-1 gutter-20">
       <dl class="span-1">
-        <dt>Characteristics</dt>
+        <dt>Characteristic Measurements</dt>
         <dd>
           {{
             protected/strains/measurements-table
-            strain=strain
+            measurements=strain.measurements
             canEdit=false
             canAdd=false
           }}

app/pods/protected/strains/strain-form/component.js

@@ -1,7 +1,7 @@
 import Ember from 'ember';
 import SetupMetaData from '../../../../mixins/setup-metadata';
 
-const { Component } = Ember;
+const { Component, computed: { sort } } = Ember;
 
 export default Component.extend(SetupMetaData, {
   // Read-only attributes
@@ -9,18 +9,22 @@ export default Component.extend(SetupMetaData, {
   isNew: null,
   isDirty: false,
   speciesList: null,
-  allCharacteristics: null,
+  allCharacteristics: [],
+  updateQueue: [],
+  deleteQueue: [],
 
   // Actions
   "on-save": null,
   "on-cancel": null,
   "on-update": null,
-  "add-characteristic": null,
-  "save-measurement": null,
-  "delete-measurement": null,
+  "add-measurements": null,
+
+  // CPs
+  sortParams: ['sortOrder'],
+  sortedSpeciesList: sort('speciesList', 'sortParams'),
 
   // Property mapping
-  propertiesList: ['strainName', 'typeStrain', 'species', 'isolatedFrom', 'accessionNumbers', 'genbank', 'wholeGenomeSequence', 'notes'],
+  propertiesList: ['strainName', 'typeStrain', 'species', 'isolatedFrom', 'accessionNumbers', 'genbank', 'wholeGenomeSequence', 'notes', 'measurements'],
   strainName: null,
   typeStrain: null,
   species: null,
@@ -29,15 +33,55 @@ export default Component.extend(SetupMetaData, {
   genbank: null,
   wholeGenomeSequence: null,
   notes: null,
+  measurements: [],
+
+  // Dropdown menu
+  characteristics: [],
+  charSortParams: ['characteristicTypeName', 'sortOrder', 'characteristicName'],
+  sortedCharacteristics: sort('characteristics', 'charSortParams'),
+  setupCharacteristics: Ember.on('init', function() {
+    const tempArray = this._resetArray(this.get('allCharacteristics'));
+    this.set('characteristics', tempArray);
+  }),
 
   resetOnInit: Ember.on('init', function() {
+    this._resetProperties();
+  }),
+
+  _resetArray: function(arr) {
+    let tempArray = [];
+    arr.forEach((val) => {
+      if (!val.get('isNew')) {
+        tempArray.push(val);
+      }
+    });
+    return tempArray;
+  },
+
+  _resetProperties: function() {
+    // Still some coupling going on here because of adding strain to measurement
+    this.get('measurements').forEach((val) => {
+      if (val.get('hasDirtyAttributes')) {
+        val.rollbackAttributes();
+      }
+      if (val.get('isNew')) {
+        this.get('strain.measurements').removeObject(val);
+      }
+    });
     this.get('propertiesList').forEach((field) => {
       const valueInStrain = this.get('strain').get(field);
-      this.set(field, valueInStrain);
+      if (field === 'measurements') {
+        const tempArray = this._resetArray(valueInStrain);
+        this.set(field, tempArray);
+      } else {
+        this.set(field, valueInStrain);
+      }
     });
+    this.set('updateQueue', []);
+    this.set('deleteQueue', []);
     // Read-only attributes
     this.set('isNew', this.get('strain.isNew'));
-  }),
+  },
 
   updateField: function(property, value) {
     this.set(property, value);
@@ -51,23 +95,32 @@ export default Component.extend(SetupMetaData, {
 
   actions: {
     save: function() {
-      return this.attrs['on-save'](this.getProperties(this.get('propertiesList')));
+      return this.attrs['on-save'](this.getProperties(this.get('propertiesList')), this.get('deleteQueue'), this.get('updateQueue'));
     },
 
     cancel: function() {
+      this._resetProperties();
       return this.attrs['on-cancel']();
     },
 
-    addCharacteristic: function() {
-      return this.attrs['add-characteristic']();
+    addMeasurement: function() {
+      const measurement = this.attrs['add-measurement']();
+      this.get('measurements').pushObject(measurement);
     },
 
     saveMeasurement: function(measurement, properties) {
-      return this.attrs['save-measurement'](measurement, properties);
+      measurement.setProperties(properties);
+      measurement.set('strain', this.get('strain'));
+      if (!measurement.get('isNew')) {
+        this.get('updateQueue').pushObject(measurement);
+      }
+      this.set('isDirty', true);
     },
 
     deleteMeasurement: function(measurement) {
-      return this.attrs['delete-measurement'](measurement);
+      this.get('deleteQueue').pushObject(measurement);
+      this.get('measurements').removeObject(measurement);
+      this.set('isDirty', true);
     },
 
     strainNameDidChange: function(value) {
@@ -100,7 +153,7 @@ export default Component.extend(SetupMetaData, {
     },
 
     notesDidChange: function(value) {
-      this.updateField('strain.notes', value);
+      this.updateField('notes', value);
     },
   },
 });

app/pods/protected/strains/strain-form/template.hbs

@@ -15,11 +15,13 @@
     <div data-row-span="2">
       <div data-field-span="2">
         <label>Species</label>
-        <select onchange={{action "speciesDidChange" value="target.value"}}>
-          {{#each speciesList as |speciesChoice|}}
-            <option value={{speciesChoice.id}} selected={{equal species.id speciesChoice.id}}>{{speciesChoice.speciesName}}</option>
-          {{/each}}
-        </select>
+        {{
+          x-select
+          options=sortedSpeciesList
+          nameAttr='speciesName'
+          selected=species.id
+          update=(action "speciesDidChange")
+        }}
       </div>
     </div>
     <div data-row-span="2">
@@ -28,7 +30,7 @@
         {{text-editor value=isolatedFrom update=(action "isolatedFromDidChange")}}
       </div>
     </div>
-    <div data-row-span="3">
+    <div data-row-span="2">
       <div data-field-span="1">
         <label>Accession Numbers</label>
         {{one-way-input type="text" class="accession-numbers" value=accessionNumbers update=(action "accessionNumbersNameDidChange")}}
@@ -37,6 +39,8 @@
         <label>GenBank</label>
         {{one-way-input type="text" class="genbank" value=genbank update=(action "genbankDidChange")}}
       </div>
+    </div>
+    <div data-row-span="1">
       <div data-field-span="1">
         <label>Whole Genome Sequence</label>
         {{one-way-input type="text" class="whole-genome-sequenc" value=wholeGenomeSequence update=(action "wholeGenomeSequenceDidChange")}}
@@ -49,18 +53,24 @@
       </div>
     </div>
   </fieldset>
-  <div>
-    {{
-      protected/strains/measurements-table
-      strain=strain
-      add-characteristic=(action "addCharacteristic")
-      allCharacteristics=allCharacteristics
-      save-measurement=(action "saveMeasurement")
-      delete-measurement=(action "deleteMeasurement")
-      canEdit=strain.canEdit
-      canAdd=metaData.canAdd
-    }}
-  </div>
+  {{#if isNew}}
+    <div>
+      Please save before adding measurements
+    </div>
+  {{else}}
+    <div>
+      {{
+        protected/strains/measurements-table
+        measurements=measurements
+        add-measurement=(action "addMeasurement")
+        allCharacteristics=sortedCharacteristics
+        save-measurement=(action "saveMeasurement")
+        delete-measurement=(action "deleteMeasurement")
+        canEdit=strain.canEdit
+        canAdd=metaData.canAdd
+      }}
+    </div>
+  {{/if}}
   <br>
   <a class="button-red smaller" {{action 'cancel'}}>
     Cancel

app/pods/protected/users/changepassword/controller.js

@@ -5,18 +5,23 @@ const { Controller, inject: { service } } = Ember;
 export default Controller.extend({
   session: service(),
   ajax: service(),
+  ajaxError: service('ajax-error'),
   currentUser: service('session-account'),
 
   actions: {
     save: function(password) {
       const id = this.get('currentUser.account.id');
       const data = { id: id, password: password };
-      this.get('ajax').post('/users/password', { data: data });
-      this.transitionToRoute('protected.users.show', id);
-      this.get('flashMessages').information('Your password has been changed.');
+      this.get('ajax').post('/users/password', { data: data }).then(() => {
+        this.transitionToRoute('protected.users.show', id);
+        this.get('flashMessages').information('Your password has been changed.');
+      }, (errors) => {
+        this.get('ajaxError').alert(errors);
+      });
     },
 
     cancel: function() {
+      this.get('flashMessages').clearMessages();
       this.transitionToRoute('protected.users.show', this.get('currentUser.account.id'));
     },
   },

app/pods/protected/users/index/route.js

@@ -11,6 +11,8 @@ export default Route.extend({
       if (!user.get('isAdmin')) {
         this.transitionTo('protected.index');
       }
+    }, () => {
+      this.transitionTo('protected.index');
     });
   },
 

app/pods/protected/users/show/route.js

@@ -15,11 +15,13 @@ export default Route.extend({
       if (!user.get('isAdmin') && user.get('id') !== user_id) {
         this.transitionTo('protected.users.index');
       }
+    }, () => {
+      this.transitionTo('protected.users.index');
     });
   },
 
   model: function(params) {
-    return this.store.findRecord('user', params.user_id);
+    return this.store.findRecord('user', params.user_id, { reload: true });
   },
 
 });

app/serializers/application.js

@@ -5,24 +5,41 @@ const { RESTSerializer } = DS;
 const { isNone } = Ember;
 
 export default RESTSerializer.extend({
-  isNewSerializerAPI: true,
-
   serializeBelongsTo: function(snapshot, json, relationship) {
-    let key = relationship.key;
-    const belongsTo = snapshot.belongsTo(key);
-    key = this.keyForRelationship ? this.keyForRelationship(key, "belongsTo", "serialize") : key;
-    json[key] = isNone(belongsTo) ? belongsTo : +belongsTo.record.id;
+    const key = relationship.key;
+    if (this._canSerialize(key)) {
+      const belongsToId = snapshot.belongsTo(key, { id: true });
+      let payloadKey = this._getMappedKey(key, snapshot.type);
+      if (payloadKey === key && this.keyForRelationship) {
+        payloadKey = this.keyForRelationship(key, "belongsTo", "serialize");
+      }
+      if (isNone(belongsToId)) {
+        json[payloadKey] = null;
+      } else {
+        json[payloadKey] = +belongsToId;
+      }
+
+      if (relationship.options.polymorphic) {
+        this.serializePolymorphicType(snapshot, json, relationship);
+      }
+    }
   },
 
   serializeHasMany: function(snapshot, json, relationship) {
-    let key = relationship.key;
-    const hasMany = snapshot.hasMany(key);
-    key = this.keyForRelationship ? this.keyForRelationship(key, "hasMany", "serialize") : key;
-
-    json[key] = [];
-    hasMany.forEach((item) => {
-      json[key].push(+item.id);
-    });
+    const key = relationship.key;
+    if (this._shouldSerializeHasMany(snapshot, key, relationship)) {
+      const hasMany = snapshot.hasMany(key, { ids: true });
+      if (hasMany !== undefined) {
+        let payloadKey = this._getMappedKey(key, snapshot.type);
+        if (payloadKey === key && this.keyForRelationship) {
+          payloadKey = this.keyForRelationship(key, "hasMany", "serialize");
+        }
+        json[payloadKey] = [];
+        hasMany.forEach((item) => {
+          json[payloadKey].push(+item);
+        });
+      }
+    }
   },
 
 });

app/services/ajax-error.js

@@ -0,0 +1,19 @@
+import Ember from 'ember';
+
+const { Service, inject: { service } } = Ember;
+
+export default Service.extend({
+  flashMessages: service(),
+
+  alert: function(error) {
+    const flash = this.get('flashMessages');
+
+    flash.clearMessages();
+    window.scrollTo(0,0);
+    error.errors.forEach((error) => {
+      console.error(error);
+      const source = error.source.pointer.split('/');
+      flash.error(`${source[source.length-1].replace(/([A-Z])/g, ' $1').capitalize()} - ${error.detail}`);
+    });
+  }
+});

app/services/globals.js

@@ -0,0 +1,9 @@
+import Ember from 'ember';
+import config from '../config/environment';
+
+const { Service } = Ember;
+
+export default Service.extend({
+  genus: config.APP.genus,
+  apiURL: config.apiURL,
+});

bower.json

@@ -2,27 +2,25 @@
   "name": "hymenobacterdotinfo",
   "dependencies": {
     "jquery": "~2.1.1",
-    "ember": "1.13.10",
+    "ember": "~2.2.0",
     "ember-cli-shims": "0.0.6",
     "ember-cli-test-loader": "0.2.1",
-    "ember-data": "1.13.15",
+    "ember-data": "~2.2.1",
     "ember-load-initializers": "0.1.7",
     "ember-qunit": "0.4.16",
     "ember-qunit-notifications": "0.1.0",
     "ember-resolver": "~0.1.20",
-    "loader.js": "ember-cli/loader.js#3.2.1",
+    "loader.js": "ember-cli/loader.js#3.4.0",
     "qunit": "~1.20.0",
     "flakes": "~1.0.0",
     "moment": "~2.10.6",
-    "select2": "3.5.2",
+    "select2": "4.0.1-rc.1",
     "antiscroll": "git://github.com/azirbel/antiscroll.git#90391fb371c7be769bc32e7287c5271981428356",
     "jquery-mousewheel": "~3.1.4",
     "jquery-ui": "~1.11.4",
     "quill": "~0.19.14",
     "pretender": "~0.10.1",
     "lodash": "~3.7.0",
-    "Faker": "~3.0.0",
-    "selectize": "~0.12.1",
-    "jQuery UI Sortable": "jquery-ui-sortable#*"
+    "Faker": "~3.0.0"
   }
 }

config/environment.js

@@ -29,7 +29,7 @@ module.exports = function(environment) {
       'script-src': "'self'",
       'font-src': "'self'",
       'connect-src': "'self'",
-      'img-src': "'self'",
+      'img-src': "'self' data:",
       'style-src': "'self' 'unsafe-inline'",
       'media-src': "'self'"
     }
@@ -61,7 +61,7 @@ module.exports = function(environment) {
   }
 
   ENV.apiURL = apiURL;
-  ENV.contentSecurityPolicy['connect-src'] = `'self' ${apiURL}`;
+  ENV.contentSecurityPolicy['connect-src'] = "'self' " + apiURL;
 
   return ENV;
 };

ember-cli-build.js

@@ -14,8 +14,8 @@ module.exports = function(defaults) {
   // quill
   app.import('bower_components/quill/dist/quill.base.css');
   app.import('bower_components/quill/dist/quill.snow.css');
-  // selectize
-  app.import('bower_components/selectize/dist/css/selectize.default.css');
+  // select2
+  app.import('bower_components/select2/dist/css/select2.min.css');
 
   // LIBS ////////////////////////////////////////////////////////////////////////
   // flakes (and deps)
@@ -27,10 +27,8 @@ module.exports = function(defaults) {
   app.import('bower_components/moment/moment.js');
   // quill
   app.import('bower_components/quill/dist/quill.min.js');
-  // jquery ui sortable
-  app.import('bower_components/jQuery UI Sortable/jquery-ui-sortable.min.js');
-  // selectize
-  app.import('bower_components/selectize/dist/js/standalone/selectize.min.js');
+  // select2
+  app.import('bower_components/select2/dist/js/select2.full.min.js');
 
   return app.toTree();
 };

package.json

@@ -10,7 +10,11 @@
   "scripts": {
     "build": "ember build",
     "start": "ember server",
-    "test": "ember test"
+    "test": "ember test",
+    "bower": "bower",
+    "ember": "ember",
+    "firebase": "firebase",
+    "deployProd": "firebase deploy -e prod"
   },
   "repository": "",
   "engines": {
@@ -20,7 +24,7 @@
   "license": "MIT",
   "devDependencies": {
     "broccoli-asset-rev": "^2.2.0",
-    "ember-cli": "1.13.11",
+    "ember-cli": "1.13.13",
     "ember-cli-app-version": "^1.0.0",
     "ember-cli-babel": "^5.1.5",
     "ember-cli-content-security-policy": "0.4.0",
@@ -33,13 +37,16 @@
     "ember-cli-mirage": "0.1.11",
     "ember-cli-qunit": "^1.0.4",
     "ember-cli-release": "0.2.8",
-    "ember-cli-sri": "^1.1.0",
+    "ember-cli-sri": "^1.2.0",
     "ember-cli-uglify": "^1.2.0",
-    "ember-data": "1.13.15",
+    "ember-data": "~2.2.1",
     "ember-disable-proxy-controllers": "^1.0.1",
     "ember-export-application-global": "^1.0.4",
     "ember-one-way-input": "0.1.3",
-    "ember-select-2": "1.3.0",
-    "ember-simple-auth": "1.0.0"
+    "ember-simple-auth": "1.0.1"
+  },
+  "dependencies": {
+    "bower": "^1.8.8",
+    "firebase-tools": "^7.12.1"
   }
 }

tests/acceptance/characteristics-test.js

@@ -6,10 +6,10 @@ import { authenticateSession } from '../helpers/ember-simple-auth';
 module('Acceptance | characteristics', {
   beforeEach: function() {
     this.application = startApp();
+    server.create('users', { role: 'A', canEdit: true, sub: 1 });
     authenticateSession(this.application, {
       access_token: "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJiYWN0ZGIiLCJzdWIiOiIxIiwiZXhwIjoxNDQ2NTAyMjI2LCJpYXQiOjE0NDY0OTg2MjZ9.vIjKHAsp2TkCV505EbtCo2xQT-2oQkB-Nv5y0b6E7Mg"
     });
-    server.create('users', { role: 'A', canEdit: true });
   },
 
   afterEach: function() {
@@ -70,3 +70,22 @@ test('creating /characteristics/new', function(assert) {
     });
   });
 });
+
+test('deleting /characteristics/:id', function(assert) {
+  const characteristic = server.create('characteristics', { 'canEdit': true });
+  visit(`/characteristics/${characteristic.id}`);
+
+  andThen(function() {
+    assert.equal(currentURL(), `/characteristics/${characteristic.id}`);
+    click('button.delete');
+
+    andThen(function() {
+      click('button.delete-confirm');
+
+      andThen(function() {
+        assert.equal(currentURL(), `/characteristics`);
+        assert.equal(server.db.characteristics.length, 0);
+      });
+    });
+  });
+});

tests/acceptance/species-test.js

@@ -6,10 +6,10 @@ import { authenticateSession } from '../helpers/ember-simple-auth';
 module('Acceptance | species', {
   beforeEach: function() {
     this.application = startApp();
+    server.create('users', { role: 'A', canEdit: true, sub: 1 });
     authenticateSession(this.application, {
       access_token: "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJiYWN0ZGIiLCJzdWIiOiIxIiwiZXhwIjoxNDQ2NTAyMjI2LCJpYXQiOjE0NDY0OTg2MjZ9.vIjKHAsp2TkCV505EbtCo2xQT-2oQkB-Nv5y0b6E7Mg"
     });
-    server.create('users', { role: 'A', canEdit: true });
   },
 
   afterEach: function() {
@@ -69,3 +69,22 @@ test('creating /species/new', function(assert) {
     });
   });
 });
+
+test('deleting /species/:id', function(assert) {
+  const species = server.create('species', { 'canEdit': true });
+  visit(`/species/${species.id}`);
+
+  andThen(function() {
+    assert.equal(currentURL(), `/species/${species.id}`);
+    click('button.delete');
+
+    andThen(function() {
+      click('button.delete-confirm');
+
+      andThen(function() {
+        assert.equal(currentURL(), `/species`);
+        assert.equal(server.db.species.length, 0);
+      });
+    });
+  });
+});

tests/acceptance/strains-test.js

@@ -6,10 +6,10 @@ import { authenticateSession } from '../helpers/ember-simple-auth';
 module('Acceptance | strains', {
   beforeEach: function() {
     this.application = startApp();
+    server.create('users', { role: 'A', canEdit: true, sub: 1 });
     authenticateSession(this.application, {
       access_token: "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJiYWN0ZGIiLCJzdWIiOiIxIiwiZXhwIjoxNDQ2NTAyMjI2LCJpYXQiOjE0NDY0OTg2MjZ9.vIjKHAsp2TkCV505EbtCo2xQT-2oQkB-Nv5y0b6E7Mg"
     });
-    server.create('users', { role: 'A', canEdit: true });
   },
 
   afterEach: function() {
@@ -74,3 +74,23 @@ test('creating /strains/new', function(assert) {
     });
   });
 });
+
+test('deleting /strains/:id', function(assert) {
+  const species = server.create('species');
+  const strain = server.create('strains', { canEdit: true , species: species.id });
+  visit(`/strains/${strain.id}`);
+
+  andThen(function() {
+    assert.equal(currentURL(), `/strains/${strain.id}`);
+    click('button.delete');
+
+    andThen(function() {
+      click('button.delete-confirm');
+
+      andThen(function() {
+        assert.equal(currentURL(), `/strains`);
+        assert.equal(server.db.strains.length, 0);
+      });
+    });
+  });
+});

tests/acceptance/users-test.js

@@ -6,10 +6,10 @@ import { invalidateSession, authenticateSession } from '../helpers/ember-simple-
 module('Acceptance | users', {
   beforeEach: function() {
     this.application = startApp();
+    server.create('users', { role: 'A', canEdit: true, sub: 1 });
     authenticateSession(this.application, {
       access_token: "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJiYWN0ZGIiLCJzdWIiOiIxIiwiZXhwIjoxNDQ2NTAyMjI2LCJpYXQiOjE0NDY0OTg2MjZ9.vIjKHAsp2TkCV505EbtCo2xQT-2oQkB-Nv5y0b6E7Mg"
     });
-    server.create('users', { role: 'A', canEdit: true });
   },
 
   afterEach: function() {

tests/unit/initializers/global-variables-test.js

@@ -1,23 +0,0 @@
-import Ember from 'ember';
-import { initialize } from '../../../initializers/global-variables';
-import { module, test } from 'qunit';
-
-var container, application;
-
-module('Unit | Initializer | global variables', {
-  beforeEach: function() {
-    Ember.run(function() {
-      application = Ember.Application.create();
-      container = application.__container__;
-      application.deferReadiness();
-    });
-  }
-});
-
-// Replace this with your real tests.
-test('it works', function(assert) {
-  initialize(container, application);
-
-  // you would normally confirm the results of the initializer here
-  assert.ok(true);
-});