update merge from master

app/initializers/component-store.js

@@ -1,5 +1,5 @@
 export function initialize(container, application) {
-  application.inject('component', 'store', 'store:main');
+  application.inject('component', 'store', 'service:store');
 }
 
 export default {

app/initializers/custom-session.js

@@ -0,0 +1,25 @@
+import Session from 'simple-auth/session';
+import parseBase64 from '../utils/parse-base64';
+import Ember from 'ember';
+
+var CustomSession = Session.extend({
+  currentUser: function() {
+    let token = this.get('secure.token');
+    if (!Ember.isEmpty(token)) {
+      let t = parseBase64(token);
+      return this.container.lookup('store:main').find('user', t['sub']);
+    }
+    return null;
+  }.property('secure.token'),
+
+});
+
+export function initialize(container, application) {
+  application.register('session:custom', CustomSession);
+}
+
+export default {
+  name: 'custom-session',
+  before: 'simple-auth',
+  initialize: initialize
+};

app/initializers/global-variables.js

@@ -7,10 +7,10 @@ var globals = Ember.Object.extend({
 });
 
 export function initialize(container, application) {
-  application.register('global:variables', globals, {singleton: true});
+  application.register('service:globals', globals, {singleton: true});
-  application.inject('controller', 'globals', 'global:variables');
+  application.inject('controller', 'globals', 'service:globals');
-  application.inject('component', 'globals', 'global:variables');
+  application.inject('component', 'globals', 'service:globals');
-  application.inject('adapter', 'globals', 'global:variables');
+  application.inject('adapter', 'globals', 'service:globals');
 }
 
 export default {

app/models/characteristic-type.js

@@ -1,13 +0,0 @@
-import DS from 'ember-data';
-
-export default DS.Model.extend({
-  characteristicTypeName: DS.attr('string'),
-  characteristics: DS.hasMany('characteristic', { async: true }),
-  createdAt: DS.attr('date'),
-  updatedAt: DS.attr('date'),
-  deletedAt: DS.attr('date'),
-  createdBy: DS.attr('number'),
-  updatedBy: DS.attr('number'),
-  deletedBy: DS.attr('number'),
-  sortOrder: DS.attr('number'),
-});

app/models/characteristic.js

@@ -1,15 +1,15 @@
 import DS from 'ember-data';
 
 export default DS.Model.extend({
-  characteristicName: DS.attr('string'),
+  characteristicName    : DS.attr('string'),
-  characteristicType: DS.belongsTo('characteristicType', { async: true }),
+  characteristicTypeName: DS.attr('string'),
-  strains           : DS.hasMany('strain', { async: true }),
+  strains               : DS.hasMany('strain', { async: true }),
-  measurements      : DS.hasMany('measurements', { async: true }),
+  measurements          : DS.hasMany('measurements', { async: true }),
-  createdAt         : DS.attr('date'),
+  createdAt             : DS.attr('date'),
-  updatedAt         : DS.attr('date'),
+  updatedAt             : DS.attr('date'),
-  deletedAt         : DS.attr('date'),
+  deletedAt             : DS.attr('date'),
-  createdBy         : DS.attr('number'),
+  createdBy             : DS.attr('number'),
-  updatedBy         : DS.attr('number'),
+  updatedBy             : DS.attr('number'),
-  deletedBy         : DS.attr('number'),
+  deletedBy             : DS.attr('number'),
-  sortOrder         : DS.attr('number'),
+  sortOrder             : DS.attr('number'),
 });

app/models/species.js

@@ -16,6 +16,7 @@ export default DS.Model.extend({
   updatedBy   : DS.attr('number'),
   deletedBy   : DS.attr('number'),
   sortOrder   : DS.attr('number'),
+  canEdit     : DS.attr('boolean'),
 
   speciesNameMU: function() {
     return Ember.String.htmlSafe(`<em>${this.get('speciesName')}</em>`);

app/models/strain.js

@@ -19,6 +19,7 @@ export default DS.Model.extend({
   deletedBy          : DS.attr('number'),
   totalMeasurements  : DS.attr('number'),
   sortOrder          : DS.attr('number'),
+  canEdit            : DS.attr('boolean'),
 
   strainNameMU: function() {
     let type = this.get('typeStrain') ? '<sup>T</sup>' : '';

app/pods/application/adapter.js

@@ -20,7 +20,7 @@ export default DS.RESTAdapter.extend({
         errors = {};
       if (response.errors !== undefined) {
         var jsonErrors = response.errors;
-        Ember.EnumerableUtils.forEach(Ember.keys(jsonErrors), function(key) {
+        Ember.EnumerableUtils.forEach(Object.keys(jsonErrors), function(key) {
           errors[Ember.String.camelize(key)] = jsonErrors[key];
         });
       }

app/pods/application/template.hbs

@@ -1,51 +0,0 @@
-  <div class="flakes-navigation">
-    {{site-logo}}
-    {{#if session.isAuthenticated}}
-      <ul>
-        {{#link-to 'compare' tagName='li' href=false}}
-          {{link-to 'Compare' 'compare'}}
-        {{/link-to}}
-        {{#link-to 'measurements' tagName='li' href=false}}
-          {{link-to 'Measurements' 'measurements'}}
-        {{/link-to}}
-        {{#link-to 'characteristics' tagName='li' href=false}}
-          {{link-to 'Characteristics' 'characteristics'}}
-        {{/link-to}}
-        {{#link-to 'species' tagName='li' href=false}}
-          {{link-to 'Species' 'species'}}
-        {{/link-to}}
-        {{#link-to 'strains' tagName='li' href=false}}
-          {{link-to 'Strains' 'strains'}}
-        {{/link-to}}
-        {{#link-to 'about' tagName='li' href=false}}
-          {{link-to 'About' 'about'}}
-        {{/link-to}}
-      </ul>
-      <p class="foot">
-        {{session.currentUser.name}}<br>
-        <a {{action 'invalidateSession'}}>Logout</a>
-      </p>
-    {{else}}
-      <p class="foot">
-        {{link-to 'Login' 'login'}}
-        <br>
-        {{link-to 'Sign Up' 'users.new'}}
-      </p>
-    {{/if}}
-  </div>
-
-  <div class="flakes-content">
-    <div class="flakes-mobile-top-bar">
-      {{site-logo}}
-      <a href="" class="navigation-expand-target">
-        <img src="img/navigation-expand-target.png" height="26px">
-      </a>
-    </div>
-
-    <div class="view-wrap">
-      {{#each flashMessages.queue as |flash|}}
-        {{custom-flash-message flash=flash}}
-      {{/each}}
-      {{outlet}}
-    </div>
-  </div>

app/pods/application/view.js

@@ -1,9 +0,0 @@
-import Ember from 'ember';
-/* global FlakesFrame */
-
-export default Ember.View.extend({
-  classNames: ['flakes-frame'],
-  didInsertElement: function() {
-    FlakesFrame.init();
-  }
-});

app/pods/characteristics/controller.js

@@ -1,6 +0,0 @@
-import Ember from 'ember';
-
-export default Ember.Controller.extend({
-  sortParams: ['characteristicType.characteristicTypeName', 'characteristicName'],
-  sortedCharacteristics: Ember.computed.sort('characteristics', 'sortParams'),
-});

app/pods/characteristics/route.js

@@ -1,15 +0,0 @@
-import Ember from 'ember';
-import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
-
-export default Ember.Route.extend(AuthenticatedRouteMixin, {
-  model: function() {
-    return Ember.RSVP.hash({
-      characteristicTypes: this.store.findAll('characteristic-type'),
-      characteristics: this.store.findAll('characteristic'),
-    });
-  },
-
-  setupController: function(controller, models) {
-    controller.setProperties(models);
-  },
-});

app/pods/compare/controller.js

@@ -1,47 +0,0 @@
-import Ember from 'ember';
-
-export default Ember.Controller.extend({
-  strains: [],
-  dataEmpty: true,
-
-  actions: {
-    search: function(selectedStrains, selectedCharacteristics) {
-      if (Ember.isEmpty(selectedStrains) || Ember.isEmpty(selectedCharacteristics)) {
-        this.set('dataEmpty', true);
-        return false;
-      }
-
-      let data = Ember.A();
-      let strains = [];
-      selectedStrains.forEach((strain) => {
-        let s = this.store.getById('strain', strain);
-        strains.pushObject(s);
-      });
-      this.set('strains', strains);
-
-      this.store.find('measurement', {
-        strain: selectedStrains,
-        characteristic: selectedCharacteristics,
-      }).then((measurements) => {
-        selectedCharacteristics.forEach((characteristic) => {
-          let char = this.store.getById('characteristic', characteristic);
-          let row = {
-            characteristic: char.get('characteristicName'),
-          };
-          selectedStrains.forEach((strain) => {
-            let meas = measurements.filterBy('strain.id', strain)
-              .filterBy('characteristic.id', characteristic);
-            if (!Ember.isEmpty(meas)) {
-              row[strain] = meas[0].get('value');
-            } else {
-              row[strain] = '';
-            }
-          });
-          data.pushObject(row);
-        });
-        this.set('data', data);
-        this.set('dataEmpty', false);
-      });
-    }
-  },
-});

app/pods/compare/route.js

@@ -1,12 +0,0 @@
-import Ember from 'ember';
-import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
-
-export default Ember.Route.extend(AuthenticatedRouteMixin, {
-  resetController: function(controller, isExiting /*, transition*/) {
-    if (isExiting) {
-      controller.set('data', null);
-      controller.set('strains', null);
-      controller.set('dataEmpty', true);
-    }
-  }
-});

app/pods/components/display-errors/template.hbs

@@ -1,3 +0,0 @@
-{{#each a as |error|}}
-  <div class="flakes-message error">{{error.message}}</div>
-{{/each}}

app/pods/components/forms/species-form/component.js

@@ -5,6 +5,7 @@ export default Ember.Component.extend({
     save: function() {
       this.sendAction('save');
     },
+
     cancel: function() {
       this.sendAction('cancel');
     },

app/pods/components/forms/species-form/template.hbs

@@ -16,11 +16,11 @@
         <label>Strains</label>
         {{#each species.strains as |strain index|}}
           {{if index ","}}
-          {{#link-to 'strains.show' strain.id}}
+          {{#link-to 'protected.strains.show' strain.id}}
             {{{strain.strainNameMU}}}
           {{/link-to}}
         {{/each}}
-        {{add-button label="Add Strain" link="strains.new"}}
+        {{add-button label="Add Strain" link="protected.strains.new"}}
       </div>
     </div>
     <div data-row-span="2">
@@ -32,11 +32,11 @@
   </fieldset>
 </form>
 <br>
-{{#if species.isDirty}}
+<a class="button-red smaller" {{action 'cancel'}}>
+  Cancel
+</a>
+{{#if species.hasDirtyAttributes}}
   <a class="button-green smaller" {{action 'save'}}>
     Save
   </a>
 {{/if}}
-<a class="button-red smaller" {{action 'cancel'}}>
-  Cancel
-</a>

app/pods/components/forms/strain-form/component.js

@@ -0,0 +1,17 @@
+import Ember from 'ember';
+
+export default Ember.Component.extend({
+  actions: {
+    save: function() {
+      // Need to override the string id for some reason
+      let strain = this.get('strain');
+      let id = strain.get('species.id');
+      strain.set('species.id', +id);
+      this.sendAction('save');
+    },
+
+    cancel: function() {
+      this.sendAction('cancel');
+    },
+  }
+});

app/pods/components/forms/strain-form/template.hbs

@@ -0,0 +1,61 @@
+<form class="grid-form">
+  <fieldset>
+    <legend><em>{{strain.strainName}}</em></legend>
+    <div data-row-span="2">
+      <div data-field-span="1">
+        <label>Strain Name</label>
+        {{input value=strain.strainName}}
+      </div>
+      <div data-field-span="1">
+        <label>Type Strain?</label>
+        {{input type="checkbox" checked=strain.typeStrain}} {{if strain.typeStrain 'Yes' 'No'}}
+      </div>
+    </div>
+    <div data-row-span="2">
+      <div data-field-span="2">
+        <label>Species</label>
+          {{
+            select-2
+            content=species
+            optionLabelPath="speciesName"
+            value=strain.species
+          }}
+      </div>
+    </div>
+    <div data-row-span="2">
+      <div data-field-span="2">
+        <label>Isolated From</label>
+        {{textarea value=strain.isolatedFrom cols="70" rows="5"}}
+      </div>
+    </div>
+    <div data-row-span="3">
+      <div data-field-span="1">
+        <label>Accession Numbers</label>
+        {{input value=strain.accessionNumbers}}
+      </div>
+      <div data-field-span="1">
+        <label>GenBank</label>
+        {{input value=strain.genbank}}
+      </div>
+      <div data-field-span="1">
+        <label>Whole Genome Sequence</label>
+        {{input value=strain.wholeGenomeSequence}}
+      </div>
+    </div>
+    <div data-row-span="2">
+      <div data-field-span="2">
+        <label>Notes</label>
+        {{textarea value=strain.notes cols="70" rows="5"}}
+      </div>
+    </div>
+  </fieldset>
+</form>
+<br>
+<a class="button-red smaller" {{action 'cancel'}}>
+  Cancel
+</a>
+{{#if strain.hasDirtyAttributes}}
+  <a class="button-green smaller" {{action 'save'}}>
+    Save
+  </a>
+{{/if}}

app/pods/components/measurement-search-panel/component.js

@@ -1,50 +0,0 @@
-import Ember from 'ember';
-
-export default Ember.Component.extend({
-  classNames: ["grid-1", "gutter-50"],
-
-  setup: function() {
-    Ember.RSVP.hash({
-      species: this.store.findAll('species'),
-      strains: this.store.findAll('strain'),
-      characteristicTypes: this.store.findAll('characteristic-type'),
-      characteristics: this.store.findAll('characteristic'),
-    }).then((models) => {
-      // Set up search parameters
-      // Clean up sort order
-      let selects = [
-        { model: 'species', id: 'id', text: 'speciesNameMU',
-          children: 'strains', cid: 'id', ctext: 'strainNameMU' },
-        { model: 'characteristicTypes', id: 'id', text: 'characteristicTypeName',
-          children: 'characteristics', cid: 'id', ctext: 'characteristicName' },
-      ];
-
-      selects.forEach((item /*, index, enumerable*/) => {
-        models[item.model] = models[item.model].filter((i) => {
-          if (!Ember.isEmpty(i.get(item.children))) { return true; }
-        });
-        models[item.model] = models[item.model].sortBy('sortOrder');
-        let temp = models[item.model].map((data) => {
-          let temp_children = [];
-          let sorted_children = data.get(item.children).sortBy('sortOrder');
-          sorted_children.forEach((child) => {
-            temp_children.push({id: child.get(item.cid), text: child.get(item.ctext)});
-          });
-          return {
-            text: data.get(item.text),
-            children: temp_children,
-          };
-        });
-        this.set(item.model, temp);
-      });
-    });
-  }.on('init'),
-
-  actions: {
-    search: function() {
-      let strains = this.get('selectedStrains'),
-          characteristics = this.get('selectedCharacteristics');
-      this.sendAction('search', strains, characteristics);
-    },
-  },
-});

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

@@ -1,13 +0,0 @@
-import Ember from 'ember';
-
-export default Ember.Component.extend({
-  isLoading: false,
-  buttonText: 'Search',
-  actions: {
-    showLoading: function() {
-      if (!this.get('isLoading')) {
-        this.sendAction('action');
-      }
-    }
-  }
-});

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

@@ -1,7 +0,0 @@
-<a class="action button-gray smaller right" {{action 'showLoading'}}>
-  {{#if isLoading}}
-    LOADING
-  {{else}}
-    {{buttonText}}
-  {{/if}}
-</a>

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

@@ -0,0 +1,3 @@
+import Ember from 'ember';
+
+export default Ember.Component.extend({});

app/pods/components/site-logo/template.hbs

@@ -1,3 +1,3 @@
-{{#link-to 'index' class='logo'}}
+{{#link-to 'protected.index' class='logo'}}
   <h2>{{globals.genus}}.info</h2>
 {{/link-to}}

app/pods/components/strain-details/component.js

@@ -1,20 +0,0 @@
-import Ember from 'ember';
-import userCanEdit from '../../../utils/user-can-edit';
-
-export default Ember.Component.extend({
-  classNames: ['grid-1'],
-  isEditing: false,
-
-  canEdit: function() {
-    return userCanEdit(this.get('session.currentUser'), this.get('strain.createdBy'));
-  }.property('session.currentUser', 'strain.createdBy').readOnly(),
-
-  actions: {
-    save: function() {
-      this.sendAction('save');
-    },
-    cancel: function() {
-      this.sendAction('cancel');
-    },
-  }
-});

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

@@ -1,145 +0,0 @@
-<div class="span-1">
-  <fieldset class="flakes-information-box {{if isEditing 'is-editing'}}">
-    <legend>
-      Strain
-        {{#if isEditing}}
-          {{input value=strain.strainName}}
-        {{else}}
-          {{strain.strainNameMU}}
-        {{/if}}
-        {{display-errors a=strain.errors.strainName}}
-    </legend>
-
-    {{! ROW 1 }}
-    <div class="grid-4 gutter-50">
-      <dl class="span-2">
-        <dt>Species</dt>
-        <dd>
-          {{#if isEditing}}
-            {{
-              select-2
-              content=species
-              optionLabelPath="speciesName"
-              value=strain.species
-            }}
-          {{else}}
-            {{#link-to 'species.show' strain.species}}
-              <em>{{strain.species.speciesName}}</em>
-            {{/link-to}}
-          {{/if}}
-        </dd>
-      </dl>
-      <dl class="span-2">
-        <dt>Type Strain?</dt>
-        <dd>
-          {{#if isEditing}}
-            {{input type="checkbox" checked=strain.typeStrain}}
-          {{/if}}
-          {{if strain.typeStrain 'Yes' 'No'}}
-          {{display-errors a=strain.errors.typeStrain}}
-        </dd>
-      </dl>
-    </div>
-
-    {{! ROW 2 }}
-    <div class="grid-6">
-      <dl class="span-2">
-        <dt>Accession Numbers</dt>
-        <dd>
-          {{#if isEditing}}
-            {{input value=strain.accessionNumbers}}
-          {{else}}
-            {{strain.accessionNumbers}}
-          {{/if}}
-          {{display-errors a=strain.errors.accessionNumbers}}
-        </dd>
-      </dl>
-      <dl class="span-2">
-        <dt>Genbank</dt>
-        <dd>
-          {{#if isEditing}}
-            {{input value=strain.genbank}}
-          {{else}}
-            {{genbank-url genbank=strain.genbank}}
-          {{/if}}
-          {{display-errors a=strain.errors.genbank}}
-        </dd>
-      </dl>
-      <dl class="span-2">
-        <dt>Whole Genome Sequence</dt>
-        <dd>
-          {{#if isEditing}}
-            {{input value=strain.wholeGenomeSequence}}
-          {{else}}
-            {{strain.wholeGenomeSequence}}
-          {{/if}}
-          {{display-errors a=strain.errors.wholeGenomeSequence}}
-        </dd>
-      </dl>
-    </div>
-
-    {{! ROW 3 }}
-    <div class="grid-4">
-      <dl class="span-4">
-        <dt>Isolated From</dt>
-        <dd>
-          {{#if isEditing}}
-            {{textarea value=strain.isolatedFrom cols="70" rows="3"}}
-          {{else}}
-            {{strain.isolatedFrom}}
-          {{/if}}
-          {{display-errors a=strain.errors.isolatedFrom}}
-        </dd>
-      </dl>
-    </div>
-
-    {{! ROW 4 }}
-    <div class="grid-4">
-      <dl class="span-4">
-        <dt>Notes</dt>
-        <dd>
-          {{#if isEditing}}
-            {{textarea value=strain.notes cols="70" rows="3"}}
-          {{else}}
-            {{strain.notes}}
-          {{/if}}
-          {{display-errors a=strain.errors.notes}}
-        </dd>
-      </dl>
-    </div>
-
-    {{! ROW 5 }}
-    <div class="grid-4">
-      <dl class="span-1">
-        <dt>Record Created</dt>
-        <dd>{{null-time strain.createdAt 'LL'}}</dd>
-      </dl>
-      <dl class="span-1">
-        <dt>Record Updated</dt>
-        <dd>{{null-time strain.updatedAt 'LL'}}</dd>
-      </dl>
-      <dl class="span-1">
-        <dt>Record Deleted</dt>
-        <dd>{{null-time strain.deletedAt 'LL'}}</dd>
-      </dl>
-      <dl class="span-1"></dl>
-    </div>
-
-    {{! ROW 6 }}
-    {{#if canEdit}}
-      <div class="grid-4">
-        <div class="span-1">
-          {{! Does nothing ATM }}
-          <a class="smaller {{if isEditing 'button-red' 'button-gray'}}" {{action 'cancel'}}>
-            {{#if isEditing}}Cancel{{else}}Edit{{/if}}
-          </a>
-          {{#if isEditing}}
-            <a class="button-green smaller" {{action 'save'}}>
-              Save
-            </a>
-          {{/if}}
-        </div>
-      </div>
-    {{/if}}
-  </fieldset>
-</div>

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

@@ -0,0 +1,17 @@
+import Ember from 'ember';
+
+export default Ember.Component.extend({
+  classNames: ["flakes-frame"],
+
+  didInsertElement: function() {
+    FlakesFrame.init();
+  },
+
+  actions: {
+    invalidateSession: function() {
+      this.sendAction('invalidateSession');
+    },
+
+  },
+
+});

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

@@ -0,0 +1,51 @@
+<div class="flakes-navigation">
+  {{site-logo}}
+  {{#if session.isAuthenticated}}
+    <ul>
+      {{#link-to 'protected.compare' tagName='li' href=false}}
+        {{link-to 'Compare' 'protected.compare'}}
+      {{/link-to}}
+      {{#link-to 'protected.measurements' tagName='li' href=false}}
+        {{link-to 'Measurements' 'protected.measurements'}}
+      {{/link-to}}
+      {{#link-to 'protected.characteristics' tagName='li' href=false}}
+        {{link-to 'Characteristics' 'protected.characteristics'}}
+      {{/link-to}}
+      {{#link-to 'protected.species' tagName='li' href=false}}
+        {{link-to 'Species' 'protected.species'}}
+      {{/link-to}}
+      {{#link-to 'protected.strains' tagName='li' href=false}}
+        {{link-to 'Strains' 'protected.strains'}}
+      {{/link-to}}
+      {{#link-to 'protected.about' tagName='li' href=false}}
+        {{link-to 'About' 'protected.about'}}
+      {{/link-to}}
+    </ul>
+    <p class="foot">
+      {{session.currentUser.name}}<br>
+      <a {{action 'invalidateSession'}}>Logout</a>
+    </p>
+  {{else}}
+    <p class="foot">
+      {{link-to 'Login' 'login'}}
+      <br>
+      {{link-to 'Sign Up' 'users.new'}}
+    </p>
+  {{/if}}
+</div>
+
+<div class="flakes-content">
+  <div class="flakes-mobile-top-bar">
+    {{site-logo}}
+    <a href="" class="navigation-expand-target">
+      <img src="img/navigation-expand-target.png" height="26px">
+    </a>
+  </div>
+
+  <div class="view-wrap">
+    {{#each flashMessages.queue as |flash|}}
+      {{custom-flash-message flash=flash}}
+    {{/each}}
+    {{yield}}
+  </div>
+</div>

app/pods/login/controller.js

@@ -1,5 +1,4 @@
 import Ember from 'ember';
-import parseBase64 from '../../utils/parse-base64';
 
 export default Ember.Controller.extend({
   actions: {
@@ -11,13 +10,7 @@ export default Ember.Controller.extend({
       this.set('loading', true);
       // Manually clean up because there might not be a transition
       this.get('flashMessages').clearMessages();
-      session.authenticate(authenticator, credentials).then(()=>{
+      session.authenticate(authenticator, credentials).then(null, (error)=> {
-        this.set('loading', false);
-        let t = parseBase64(session.get('secure.token'));
-        this.store.find('user', t['sub']).then((user) => {
-          session.set('currentUser', user);
-        });
-      }, (error)=> {
         this.set('loading', false);
         this.get('flashMessages').error(error.error);
       });

app/pods/login/template.hbs

@@ -1,6 +1,4 @@
-{{#if loggedIn}}
+{{#x-application invalidateSession="invalidateSession"}}
-  <p>You are already logged in!</p>
-{{else}}
   {{#if loading}}
     {{loading-panel}}
   {{else}}
@@ -11,4 +9,4 @@
         {{input class="button-gray" type="submit" value="Log In"}}
     </form>
   {{/if}}
-{{/if}}
+{{/x-application}}

app/pods/measurements/controller.js

@@ -1,50 +0,0 @@
-import Ember from 'ember';
-import ColumnDefinition from 'ember-table/models/column-definition';
-
-export default Ember.Controller.extend({
-  measurements: [],
-
-  measurementsEmpty: function() {
-    return this.get('measurements').length === 0;
-  }.property('measurements'),
-
-  tableColumns: Ember.computed(function() {
-    let strainCol = ColumnDefinition.create({
-      savedWidth: 200,
-      textAlign: 'text-align-left',
-      headerCellName: 'Strain',
-      contentPath: 'strain.fullNameMU',
-    });
-
-    let charCol = ColumnDefinition.create({
-      savedWidth: 200,
-      textAlign: 'text-align-left',
-      headerCellName: 'Characteristic',
-      contentPath: 'characteristic.characteristicName',
-    });
-
-    let valCol = ColumnDefinition.create({
-      savedWidth: 150,
-      textAlign: 'text-align-left',
-      headerCellName: 'Value',
-      contentPath: 'value',
-    });
-
-    return [strainCol, charCol, valCol];
-  }),
-
-  tableContent: Ember.computed('measurements', function() {
-    return this.get('measurements');
-  }),
-
-  actions: {
-    search: function(selectedStrains, selectedCharacteristics) {
-      this.store.find('measurement', {
-        strain: selectedStrains,
-        characteristic: selectedCharacteristics,
-      }).then((measurements)=>{
-        this.set('measurements', measurements);
-      });
-    }
-  },
-});

app/pods/measurements/template.hbs

@@ -1,21 +0,0 @@
-<h2>{{genus-name}} Measurements</h2>
-
-{{measurement-search-panel search='search' strainLabel='All strains' charLabel='All characteristics'}}
-
-<div class="grid-12 gutter-50">
-  <div class="span-12">
-    <h3>Total matching measurements: {{measurements.length}}</h3>
-  </div>
-</div>
-
-{{#if measurementsEmpty}}
-  <span>No results</span>
-{{else}}
-  {{
-    ember-table
-    columns=tableColumns
-    content=tableContent
-    columnMode='fluid'
-    hasFooter=false
-  }}
-{{/if}}

app/pods/protected/characteristics/controller.js

@@ -0,0 +1,6 @@
+import Ember from 'ember';
+
+export default Ember.Controller.extend({
+  sortParams: ['characteristicTypeName', 'sortOrder'],
+  sortedCharacteristics: Ember.computed.sort('model', 'sortParams'),
+});

app/pods/protected/characteristics/route.js

@@ -3,7 +3,7 @@ import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixi
 
 export default Ember.Route.extend(AuthenticatedRouteMixin, {
   model: function() {
-    return this.store.createRecord('species');
+    return this.store.findAll('characteristic');
   },
 
 });

app/pods/protected/characteristics/template.hbs

@@ -1,18 +1,20 @@
 <h2>{{genus-name}} Characteristics</h2>
-<h3>Total characteristics: {{characteristics.length}}</h3>
+<h3>Total characteristics: {{model.length}}</h3>
 
 <table class="flakes-table">
   <thead>
     <tr>
       <th>Name</th>
       <th>Type</th>
+      <th>Sort Order</th>
     </tr>
   </thead>
   <tbody>
     {{#each sortedCharacteristics as |row|}}
       <tr>
         <td>{{row.characteristicName}}</td>
-        <td>{{row.characteristicType.characteristicTypeName}}</td>
+        <td>{{row.characteristicTypeName}}</td>
+        <td>{{row.sortOrder}}</td>
       </tr>
     {{/each}}
   </tbody>

app/pods/protected/compare/controller.js

@@ -0,0 +1,14 @@
+import Ember from 'ember';
+
+export default Ember.Controller.extend({
+  actions: {
+    search: function() {
+      let query = {
+        strain_ids: this.get('selectedStrains'),
+        characteristic_ids: this.get('selectedCharacteristics'),
+      };
+
+      this.transitionToRoute('protected.compare.results', {queryParams: query});
+    }
+  }
+});

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

@@ -0,0 +1,50 @@
+import Ember from 'ember';
+
+export default Ember.Controller.extend({
+  queryParams: ['strain_ids', 'characteristic_ids'],
+
+  strains: function() {
+    let strains = [];
+    let strain_ids = this.get('strain_ids').split(',');
+    strain_ids.forEach((id) => {
+      strains.push(this.store.peekRecord('strain', id));
+    })
+    return strains;
+  }.property('strain_ids'),
+
+  characteristics: function() {
+    let characteristics = [];
+    let characteristic_ids = this.get('characteristic_ids').split(',');
+    characteristic_ids.forEach((id) => {
+      characteristics.push(this.store.peekRecord('characteristic', id));
+    })
+    return characteristics;
+  }.property('characteristic_ids'),
+
+  // Set up data table matrix
+  data: function() {
+    let characteristics = this.get('characteristics');
+    let strains = this.get('strains');
+    let measurements = this.get('model');
+    let data = Ember.A();
+
+    characteristics.forEach((characteristic) => {
+      let row = {
+        characteristic: characteristic.get('characteristicName'),
+      };
+
+      strains.forEach((strain) => {
+        let meas = measurements.filterBy('strain.id', strain.get('id'))
+          .filterBy('characteristic.id', characteristic.get('id'));
+        if (!Ember.isEmpty(meas)) {
+          row[strain.get('id')] = meas[0].get('value');
+        } else {
+          row[strain.get('id')] = '';
+        }
+      });
+      data.pushObject(row);
+    });
+    return data;
+  }.property('characteristics', 'strains'),
+
+});

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

@@ -0,0 +1,11 @@
+import Ember from 'ember';
+
+export default Ember.Route.extend({
+  model: function(params) {
+    let compare = this.controllerFor('protected.compare');
+    compare.set('selectedStrains', params.strain_ids);
+    compare.set('selectedCharacteristics', params.characteristic_ids);
+    return this.store.query('measurement', params);
+  },
+
+});

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

@@ -1,17 +1,3 @@
-<h2>{{genus-name}} - Compare Strains</h2>
-
-{{
-  measurement-search-panel
-  search='search'
-  strainLabel='Select one or more strains'
-  charLabel='Select one or more characteristics'
-}}
-
-{{#if dataEmpty}}
-  <div class="flakes-message information">
-    Please select one or more strains and one or more characteristics.
-  </div>
-{{else}}
 <div class="overflow-div">
   <table class="flakes-table">
     <thead>
@@ -19,7 +5,7 @@
         <th>Characteristic</th>
         {{#each strains as |strain|}}
           <th>
-            {{#link-to 'strains.show' strain.id classBinding="data.typeStrain:type-strain"}}
+            {{#link-to 'protected.strains.show' strain.id classBinding="data.typeStrain:type-strain"}}
               {{strain.fullNameMU}}
             {{/link-to}}
           </th>
@@ -38,4 +24,3 @@
     </tbody>
   </table>
 </div>
-{{/if}}

app/pods/protected/compare/route.js

@@ -0,0 +1,13 @@
+import Ember from 'ember';
+
+export default Ember.Route.extend({
+  model: function() {
+    return this.store.findAll('characteristic');
+  },
+
+  setupController: function(controller, model) {
+    controller.set('characteristics', this.store.peekAll('characteristic'));
+    controller.set('strains', this.store.peekAll('strain'));
+  },
+
+});

app/pods/protected/compare/template.hbs

@@ -1,3 +1,5 @@
+<h2>{{genus-name}} - Compare Strains</h2>
+
 <div class="span-1">
   <fieldset>
     <form>
@@ -7,10 +9,11 @@
           {{
             select-2
             multiple=true
-            content=species
+            content=strains
             value=selectedStrains
             optionValuePath="id"
-            placeholder=strainLabel
+            optionLabelPath="fullNameMU"
+            placeholder="Select one or more strains"
           }}
         </li>
         <li>
@@ -18,16 +21,21 @@
           {{
             select-2
             multiple=true
-            content=characteristicTypes
+            content=characteristics
             value=selectedCharacteristics
             optionValuePath="id"
-            placeholder=charLabel
+            optionLabelPath="characteristicName"
+            placeholder="Select one or more characteristics"
           }}
         </li>
         <li>
-          {{search-button isLoading=isLoading action='search'}}
+          <a class="action button-gray smaller right" {{action 'search'}}>
+            Search
+          </a>
         </li>
       </ul>
     </form>
   </fieldset>
 </div>
+
+{{outlet}}

app/pods/protected/index/route.js

@@ -2,7 +2,8 @@ import Ember from 'ember';
 import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
 
 export default Ember.Route.extend(AuthenticatedRouteMixin, {
-  beforeModel: function() {
+  beforeModel: function(transition) {
-    this.transitionTo('compare');
+    this._super(transition);
+    this.transitionTo('protected.compare');
   }
 });

app/pods/protected/measurements/template.hbs

@@ -0,0 +1,3 @@
+<h2>{{genus-name}} Measurements</h2>
+
+Be back soon

app/pods/protected/route.js

@@ -1,14 +1,12 @@
 import Ember from 'ember';
 import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
+import parseBase64 from '../../utils/parse-base64';
 
 export default Ember.Route.extend(AuthenticatedRouteMixin, {
   model: function() {
-    return Ember.RSVP.hash({
+    let token = this.get('session.secure.token');
-      strains: this.store.findAll('strain'),
+    let user = parseBase64(token);
-    });
+    return this.store.find('user', user.sub);
   },
 
-  setupController: function(controller, model) {
-    controller.setProperties(model);
-  },
 });

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

@@ -0,0 +1,29 @@
+import Ember from 'ember';
+
+export default Ember.Controller.extend({
+  actions: {
+    save: function() {
+      let species = this.get('model');
+
+      if (species.get('isDirty')) {
+        species.save().then((species) => {
+          this.transitionToRoute('protected.species.show', species);
+        }, (err) => {
+          this.get('flashMessages').error(err.responseJSON.error);
+        });
+      } else {
+        this.transitionToRoute('protected.species.show', species);
+      }
+    },
+
+    cancel: function() {
+      let species = this.get('model');
+
+      species.get('errors').clear();
+      species.rollback();
+
+      this.transitionToRoute('protected.species.show', species);
+    },
+
+  },
+});

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

@@ -0,0 +1,11 @@
+import Ember from 'ember';
+import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
+
+export default Ember.Route.extend(AuthenticatedRouteMixin, {
+  afterModel: function(species) {
+    if (!species.get('canEdit')) {
+      this.transitionTo('species.show', species.get('id'));
+    }
+  },
+
+});

app/pods/protected/species/index/controller.js

@@ -0,0 +1,11 @@
+import Ember from 'ember';
+
+export default Ember.Controller.extend({
+  sortParams: ['speciesName', 'strainCount'],
+  sortedSpecies: Ember.computed.sort('model', 'sortParams'),
+
+  metaData: function() {
+    return Ember.copy(this.store.metadataFor('species'));
+  }.property('model.isLoaded').readOnly(),
+
+});

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

@@ -0,0 +1,7 @@
+import Ember from 'ember';
+
+export default Ember.Route.extend({
+  model: function() {
+    return this.store.findAll('species');
+  }
+});

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

@@ -1,7 +1,7 @@
 <h2>{{genus-name}} Species</h2>
 <h3>Total species: {{model.length}}</h3>
 
-{{add-button label="Add Species" link="species.new" canAdd=metaData.canAdd}}
+{{add-button label="Add Species" link="protected.species.new" canAdd=metaData.canAdd}}
 
 <table class="flakes-table">
   <thead>
@@ -15,7 +15,7 @@
       <tr>
         <td>
           <em>
-            {{#link-to 'species.show' species}}
+            {{#link-to 'protected.species.show' species}}
               {{species.speciesName}}
             {{/link-to}}
           </em>
@@ -23,7 +23,7 @@
         <td>
           {{#each species.strains as |strain index|}}
             {{if index ","}}
-            {{#link-to 'strains.show' strain.id}}
+            {{#link-to 'protected.strains.show' strain.id}}
               {{{strain.strainNameMU}}}
             {{/link-to}}
           {{/each}}

app/pods/protected/species/new/controller.js

@@ -0,0 +1,25 @@
+import Ember from 'ember';
+
+export default Ember.Controller.extend({
+  actions: {
+    save: function() {
+      let species = this.get('model');
+
+      if (species.get('isDirty')) {
+        species.save().then((species) => {
+          this.transitionToRoute('protected.species.show', species.get('id'));
+        }, (err) => {
+          this.get('flashMessages').error(err.responseJSON.error);
+        });
+      } else {
+        species.deleteRecord();
+        this.transitionToRoute('protected.species.index');
+      }
+    },
+
+    cancel: function() {
+      this.transitionToRoute('protected.species.index');
+    },
+
+  },
+});

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

@@ -0,0 +1,27 @@
+import Ember from 'ember';
+import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
+
+export default Ember.Route.extend(AuthenticatedRouteMixin, {
+  beforeModel: function(transition) {
+    this._super(transition);
+    if (this.get('session.currentUser.role') === 'R') {
+      this.transitionTo('species.index');
+    }
+  },
+
+  model: function() {
+    return this.store.createRecord('species');
+  },
+
+  actions: {
+    willTransition: function(/*transition*/) {
+      let controller = this.get('controller');
+      let species = controller.get('model');
+
+      if (species.get('isNew')) {
+        species.deleteRecord();
+      }
+    },
+  },
+
+});

app/pods/protected/species/new/template.hbs

@@ -0,0 +1,6 @@
+{{
+  forms/species-form
+  species=model
+  save="save"
+  cancel="cancel"
+}}

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

@@ -0,0 +1,9 @@
+import Ember from 'ember';
+import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
+
+export default Ember.Route.extend(AuthenticatedRouteMixin, {
+  model: function(params) {
+    return this.store.findRecord('species', params.species_id, { reload: true });
+  },
+
+});

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

@@ -6,19 +6,22 @@
       </legend>
 
       {{! ROW 1 }}
-      <div class="grid-4">
+      <div class="grid-2 gutter-20">
-        <dl class="span-2">
+        <dl class="span-1">
           <dt>Strains</dt>
           <dd>
-            {{#each model.strains as |strain index|}}
+            <ul>
-              {{if index ","}}
+              {{#each model.strains as |strain index|}}
-              {{#link-to 'strains.show' strain.id}}
+                <li>
-                {{{strain.strainNameMU}}}
+                  {{#link-to 'protected.strains.show' strain.id}}
-              {{/link-to}}
+                    {{{strain.strainNameMU}}}
-            {{/each}}
+                  {{/link-to}}
+                </li>
+              {{/each}}
+            </ul>
           </dd>
         </dl>
-        <dl class="span-2">
+        <dl class="span-1">
           <dt>Type Species?</dt>
           <dd>
             {{if model.typeSpecies 'Yes' 'No'}}
@@ -27,8 +30,8 @@
       </div>
 
       {{! ROW 2 }}
-      <div class="grid-4">
+      <div class="grid-1 gutter-20">
-        <dl class="span-4">
+        <dl class="span-1">
           <dt>Etymology</dt>
           <dd>
             {{model.etymology}}
@@ -37,7 +40,7 @@
       </div>
 
       {{! ROW 3 }}
-      <div class="grid-4">
+      <div class="grid-3 gutter-20">
         <dl class="span-1">
           <dt>Record Created</dt>
           <dd>{{null-time model.createdAt 'LL'}}</dd>
@@ -50,14 +53,13 @@
           <dt>Record Deleted</dt>
           <dd>{{null-time model.deletedAt 'LL'}}</dd>
         </dl>
-        <dl class="span-1"></dl>
       </div>
     </fieldset>
   </div>
 </div>
-{{#if userCanEdit}}
+{{#if model.canEdit}}
   <br>
-  {{#link-to 'species.edit' model class="button-gray smaller"}}
+  {{#link-to 'protected.species.edit' model class="button-gray smaller"}}
     Edit
   {{/link-to}}
 {{/if}}

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

@@ -0,0 +1,30 @@
+import Ember from 'ember';
+
+export default Ember.Controller.extend({
+  actions: {
+    save: function() {
+      let strain = this.get('strain');
+
+      if (strain.get('isDirty')) {
+        strain.save().then((strain) => {
+          this.transitionToRoute('protected.strains.show', strain);
+        }, (err) => {
+          this.get('flashMessages').error(err.responseJSON.error);
+        });
+      } else {
+        strain.deleteRecord();
+        this.transitionToRoute('protected.strains.show', strain);
+      }
+    },
+
+    cancel: function() {
+      let strain = this.get('protected.strain');
+
+      strain.get('errors').clear();
+      strain.rollback();
+
+      this.transitionToRoute('protected.strains.show', strain);
+    },
+
+  },
+});

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

@@ -5,10 +5,18 @@ export default Ember.Route.extend(AuthenticatedRouteMixin, {
   model: function(params) {
     return Ember.RSVP.hash({
       strain: this.store.find('strain', params.strain_id),
-      species: this.store.findAll('species')
+      species: this.store.findAll('species'), // Need for dropdown
     });
   },
+
+  afterModel: function(models) {
+    if (!models.strain.get('canEdit')) {
+      this.transitionTo('strains.show', models.strain.get('id'));
+    }
+  },
+
   setupController: function(controller, models) {
     controller.setProperties(models);
   },
+
 });

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

@@ -1,8 +1,7 @@
 {{
-  strain-details
+  forms/strain-form
   strain=strain
   species=species
-  isEditing=true
   save="save"
   cancel="cancel"
 }}

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

@@ -0,0 +1,11 @@
+import Ember from 'ember';
+
+export default Ember.Controller.extend({
+  sortParams: ['fullNameMU', 'totalMeasurements'],
+  sortedStrains: Ember.computed.sort('model', 'sortParams'),
+
+  metaData: function() {
+    return Ember.copy(this.store.metadataFor('strain'));
+  }.property('model.isLoaded').readOnly(),
+
+});

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

@@ -3,6 +3,6 @@ import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixi
 
 export default Ember.Route.extend(AuthenticatedRouteMixin, {
   model: function() {
-    return this.store.findAll('measurement');
+    return this.store.findAll('strain');
   },
 });

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

@@ -1,7 +1,7 @@
 <h2>{{genus-name}} Strains</h2>
-<h3>Total strains: {{strains.length}}</h3>
+<h3>Total strains: {{model.length}}</h3>
 
-{{add-button label="Add Strain" link="strains.new"}}
+{{add-button label="Add Strain" link="protected.strains.new" canAdd=metaData.canAdd}}
 
 <table class="flakes-table">
   <thead>
@@ -14,7 +14,7 @@
     {{#each sortedStrains as |row|}}
       <tr>
         <td>
-          {{#link-to 'strains.show' row.id classBinding="data.typeStrain:type-strain"}}
+          {{#link-to 'protected.strains.show' row.id classBinding="data.typeStrain:type-strain"}}
             {{row.fullNameMU}}
           {{/link-to}}
         </td>

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

@@ -0,0 +1,24 @@
+import Ember from 'ember';
+
+export default Ember.Controller.extend({
+  actions: {
+    save: function() {
+      let strain = this.get('strain');
+
+      if (strain.get('isDirty')) {
+        strain.save().then((strain) => {
+          this.transitionToRoute('protected.strains.show', strain);
+        }, (err) => {
+          this.get('flashMessages').error(err.responseJSON.error);
+        });
+      } else {
+        this.transitionToRoute('protected.strains.index');
+      }
+    },
+
+    cancel: function() {
+      this.transitionToRoute('protected.strains.index');
+    },
+
+  },
+});

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

@@ -0,0 +1,34 @@
+import Ember from 'ember';
+import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
+
+export default Ember.Route.extend(AuthenticatedRouteMixin, {
+  beforeModel: function(transition) {
+    this._super(transition);
+    if (this.get('session.currentUser.role') === 'R') {
+      this.transitionTo('strains.index');
+    }
+  },
+
+  model: function() {
+    return Ember.RSVP.hash({
+      strain: this.store.createRecord('strain'),
+      species: this.store.findAll('species'), // Need for dropdown
+    });
+  },
+
+  setupController: function(controller, models) {
+    controller.setProperties(models);
+  },
+
+  actions: {
+    willTransition: function(/*transition*/) {
+      let controller = this.get('controller');
+      let strain = controller.get('strain');
+
+      if (strain.get('isNew')) {
+        strain.deleteRecord();
+      }
+    },
+  },
+
+});

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

@@ -1,8 +1,7 @@
 {{
-  strain-details
+  forms/strain-form
   strain=strain
   species=species
-  isEditing=isEditing
   save="save"
   cancel="cancel"
 }}

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

@@ -0,0 +1,9 @@
+import Ember from 'ember';
+import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
+
+export default Ember.Route.extend(AuthenticatedRouteMixin, {
+  model: function(params) {
+    return this.store.findRecord('strain', params.strain_id, { reload: true });
+  },
+
+});

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

@@ -0,0 +1,89 @@
+<div class="span-1">
+  <fieldset class="flakes-information-box {{if isEditing 'is-editing'}}">
+    <legend>
+      Strain {{model.strainNameMU}}
+    </legend>
+
+    {{! ROW 1 }}
+    <div class="grid-2 gutter-20">
+      <dl class="span-1">
+        <dt>Species</dt>
+        <dd>
+          {{#link-to 'protected.species.show' model.species.id}}
+            <em>{{model.species.speciesNameMU}}</em>
+          {{/link-to}}
+        </dd>
+      </dl>
+      <dl class="span-1">
+        <dt>Type Strain?</dt>
+        <dd>
+          {{if model.typeStrain 'Yes' 'No'}}
+        </dd>
+      </dl>
+    </div>
+
+    {{! ROW 2 }}
+    <div class="grid-3 gutter-20">
+      <dl class="span-1">
+        <dt>Accession Numbers</dt>
+        <dd>
+          {{model.accessionNumbers}}
+        </dd>
+      </dl>
+      <dl class="span-1">
+        <dt>Genbank</dt>
+        <dd>
+          {{genbank-url genbank=model.genbank}}
+        </dd>
+      </dl>
+      <dl class="span-1">
+        <dt>Whole Genome Sequence</dt>
+        <dd>
+          {{model.wholeGenomeSequence}}
+        </dd>
+      </dl>
+    </div>
+
+    {{! ROW 3 }}
+    <div class="grid-1 gutter-20">
+      <dl class="span-1">
+        <dt>Isolated From</dt>
+        <dd>
+          {{model.isolatedFrom}}
+        </dd>
+      </dl>
+    </div>
+
+    {{! ROW 4 }}
+    <div class="grid-1 gutter-20">
+      <dl class="span-1">
+        <dt>Notes</dt>
+        <dd>
+          {{model.notes}}
+        </dd>
+      </dl>
+    </div>
+
+    {{! ROW 5 }}
+    <div class="grid-3 gutter-20">
+      <dl class="span-1">
+        <dt>Record Created</dt>
+        <dd>{{null-time model.createdAt 'LL'}}</dd>
+      </dl>
+      <dl class="span-1">
+        <dt>Record Updated</dt>
+        <dd>{{null-time model.updatedAt 'LL'}}</dd>
+      </dl>
+      <dl class="span-1">
+        <dt>Record Deleted</dt>
+        <dd>{{null-time model.deletedAt 'LL'}}</dd>
+      </dl>
+    </div>
+  </fieldset>
+</div>
+{{#if model.canEdit}}
+  <br>
+  {{#link-to 'protected.strains.edit' model.id class="button-gray smaller"}}
+    Edit
+  {{/link-to}}
+{{/if}}

app/pods/protected/template.hbs

@@ -0,0 +1,3 @@
+{{#x-application invalidateSession="invalidateSession"}}
+  {{outlet}}
+{{/x-application}}

app/pods/strains/index/controller.js

@@ -1,6 +0,0 @@
-import Ember from 'ember';
-
-export default Ember.Controller.extend({
-  sortParams: ['fullNameMU', 'totalMeasurements'],
-  sortedStrains: Ember.computed.sort('strains', 'sortParams'),
-});

app/pods/strains/new/controller.js

@@ -1,21 +0,0 @@
-import Ember from 'ember';
-
-export default Ember.Controller.extend({
-  isEditing: true,
-  actions: {
-    save: function() {
-      var strain = this.get('strain');
-      if (strain.get('isDirty')) {
-        strain.save();
-      }
-      this.transitionToRoute('strains.index');
-    },
-    cancel: function() {
-      var strain = this.get('strain');
-      if (strain.get('isNew')) {
-        strain.deleteRecord();
-      }
-      this.transitionToRoute('strains.index');
-    }
-  }
-});

app/pods/strains/new/route.js

@@ -1,14 +0,0 @@
-import Ember from 'ember';
-import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
-
-export default Ember.Route.extend(AuthenticatedRouteMixin, {
-  model: function() {
-    return Ember.RSVP.hash({
-      strain: this.store.createRecord('strain'),
-      species: this.store.findAll('species')
-    });
-  },
-  setupController: function(controller, models) {
-    controller.setProperties(models);
-  },
-});

app/pods/strains/show/controller.js

@@ -1,19 +0,0 @@
-import Ember from 'ember';
-
-export default Ember.Controller.extend({
-  isEditing: false,
-  actions: {
-    save: function() {
-      var strain = this.get('strain');
-      if (strain.get('isDirty')) {
-        strain.save();
-      }
-      this.toggleProperty('isEditing');
-    },
-    cancel: function() {
-      this.get('strain').get('errors').clear();
-      this.get('strain').rollback();
-      this.toggleProperty('isEditing');
-    }
-  }
-});

app/pods/users/template.hbs

@@ -0,0 +1,3 @@
+{{#x-application invalidateSession="invalidateSession"}}
+  {{outlet}}
+{{/x-application}}

app/router.js

@@ -7,20 +7,7 @@ var Router = Ember.Router.extend({
 
 Router.map(function() {
   this.route('login');
-  this.route('about');
-  this.route('characteristics');
-  this.route('measurements');
-  this.route('compare');
 
-  this.route('species', function() {
-    this.route('new');
-    this.route('show', { path: ':species_id' });
-    this.route('edit', { path: ':species_id/edit' });
-  });
-  this.route('strains', function() {
-    this.route('new');
-    this.route('show', { path: ':strain_id' });
-  });
   this.route('users', function() {
     this.route('new', function() {
       this.route('fail');
@@ -28,6 +15,30 @@ Router.map(function() {
       this.route('verify', { path: ':nonce' });
     });
   });
+
+  this.route('protected', { path: '/' }, function() {
+    this.route('about');
+    this.route('characteristics');
+    this.route('measurements');
+
+    this.route('compare', function() {
+      this.route('results');
+    });
+
+    this.route('species', function() {
+      this.route('new');
+      this.route('show', { path: ':species_id' });
+      this.route('edit', { path: ':species_id/edit' });
+    });
+
+    this.route('strains', function() {
+      this.route('new');
+      this.route('show', { path: ':strain_id' });
+      this.route('edit', { path: ':strain_id/edit' });
+    });
+
+  });
+
 });
 
 export default Router;

app/serializers/strain.js

@@ -0,0 +1,14 @@
+import DS from 'ember-data';
+import Ember from 'ember';
+
+export default DS.RESTSerializer.extend({
+  isNewSerializerAPI: true,
+
+  serializeBelongsTo: function(snapshot, json, relationship) {
+    var key = relationship.key;
+    var belongsTo = snapshot.belongsTo(key);
+    key = this.keyForRelationship ? this.keyForRelationship(key, "belongsTo", "serialize") : key;
+    json[key] = Ember.isNone(belongsTo) ? belongsTo : +belongsTo.record.id;
+  }
+
+});

app/utils/user-can-add.js

@@ -1,3 +0,0 @@
-export default function userCanAdd(role) {
-  return (role === 'W') || (role === 'A');
-}

app/utils/user-can-edit.js

@@ -1,5 +0,0 @@
-export default function userCanEdit(currentUser, author) {
-  let id = currentUser.id;
-  let role = currentUser.role;
-  return (role === 'W' && (+id === author)) || (role === 'A');
-}

bower.json

@@ -2,14 +2,14 @@
   "name": "clostridiumdotinfo",
   "dependencies": {
     "jquery": "~2.1.1",
-    "ember": "1.12.0",
+    "ember": "1.13.3",
     "ember-cli-shims": "ember-cli/ember-cli-shims#0.0.3",
     "ember-cli-test-loader": "ember-cli-test-loader#0.1.3",
-    "ember-data": "1.0.0-beta.18",
+    "ember-data": "1.13.5",
-    "ember-load-initializers": "ember-cli/ember-load-initializers#0.1.4",
+    "ember-load-initializers": "ember-cli/ember-load-initializers#0.1.5",
-    "ember-qunit": "0.3.3",
+    "ember-qunit": "0.4.1",
     "ember-qunit-notifications": "0.0.7",
-    "ember-resolver": "~0.1.15",
+    "ember-resolver": "~0.1.18",
     "loader.js": "ember-cli/loader.js#3.2.0",
     "qunit": "~1.17.1",
     "flakes": "~1.0.0",

config/environment.js

@@ -16,8 +16,10 @@ module.exports = function(environment) {
     },
     podModulePrefix: 'clostridiumdotinfo/pods',
     'simple-auth': {
+      session: 'session:custom',
       authorizer: 'simple-auth-authorizer:token',
       store: 'simple-auth-session-store:local-storage',
+      routeAfterAuthentication: 'protected.index',
     },
     'simple-auth-token': {
       identificationField: 'email',

ember-cli-build.js

@@ -0,0 +1,24 @@
+/* global require, module */
+var EmberApp = require('ember-cli/lib/broccoli/ember-app');
+
+module.exports = function(defaults) {
+  var app = new EmberApp(defaults, {
+    // Add options here
+  });
+
+  // STYLES //////////////////////////////////////////////////////////////////////
+  // flakes (and deps)
+  app.import('bower_components/flakes/css/all.css');
+  app.import('bower_components/gridforms/gridforms/gridforms.css');
+
+  // LIBS ////////////////////////////////////////////////////////////////////////
+  // flakes (and deps)
+  app.import('bower_components/snapjs/snap.js');
+  app.import('bower_components/responsive-elements/responsive-elements.js');
+  app.import('bower_components/gridforms/gridforms/gridforms.js');
+  app.import('bower_components/flakes/js/base.js');
+  // moment
+  app.import('bower_components/moment/moment.js');
+
+  return app.toTree();
+};

package.json

@@ -20,25 +20,25 @@
   "license": "MIT",
   "devDependencies": {
     "broccoli-asset-rev": "^2.0.2",
-    "ember-cli": "0.2.7",
+    "ember-cli": "1.13.1",
-    "ember-cli-app-version": "0.3.3",
+    "ember-cli-app-version": "0.4.0",
     "ember-cli-babel": "^5.0.0",
     "ember-cli-content-security-policy": "0.4.0",
     "ember-cli-dependency-checker": "^1.0.0",
     "ember-cli-divshot": "^0.1.7",
     "ember-cli-flash": "1.1.4",
-    "ember-cli-htmlbars": "0.7.6",
+    "ember-cli-htmlbars": "0.7.9",
-    "ember-cli-ic-ajax": "0.1.1",
+    "ember-cli-htmlbars-inline-precompile": "^0.1.1",
+    "ember-cli-ic-ajax": "0.2.1",
     "ember-cli-inject-live-reload": "^1.3.0",
-    "ember-cli-qunit": "0.3.13",
+    "ember-cli-qunit": "0.3.15",
     "ember-cli-simple-auth": "^0.8.0",
     "ember-cli-simple-auth-token": "^0.7.2",
+    "ember-cli-release": "0.2.3",
     "ember-cli-uglify": "^1.0.1",
-    "ember-data": "1.0.0-beta.18",
+    "ember-data": "1.13.5",
     "ember-disable-proxy-controllers": "^1.0.0",
     "ember-export-application-global": "^1.0.2",
-    "ember-select-2": "1.3.0",
+    "ember-select-2": "1.3.0"
-    "ember-table": "0.5.0",
-    "glob": "^4.5.3"
   }
 }

tests/.jshintrc

@@ -26,7 +26,7 @@
   "node": false,
   "browser": false,
   "boss": true,
-  "curly": false,
+  "curly": true,
   "debug": false,
   "devel": false,
   "eqeqeq": true,
@@ -47,5 +47,6 @@
   "strict": false,
   "white": false,
   "eqnull": true,
-  "esnext": true
+  "esnext": true,
+  "unused": true
 }

tests/helpers/start-app.js

@@ -1,6 +1,5 @@
 import Ember from 'ember';
 import Application from '../../app';
-import Router from '../../router';
 import config from '../../config/environment';
 
 export default function startApp(attrs) {

tests/unit/utils/user-can-add-test.js

@@ -1,10 +0,0 @@
-import userCanAdd from '../../../utils/user-can-add';
-import { module, test } from 'qunit';
-
-module('Unit | Utility | user can add');
-
-// Replace this with your real tests.
-test('it works', function(assert) {
-  var result = userCanAdd();
-  assert.ok(result);
-});

tests/unit/utils/user-can-edit-test.js

@@ -1,10 +0,0 @@
-import userCanEdit from '../../../utils/user-can-edit';
-import { module, test } from 'qunit';
-
-module('Unit | Utility | user can edit');
-
-// Replace this with your real tests.
-test('it works', function(assert) {
-  var result = userCanEdit();
-  assert.ok(result);
-});