Pods, pods, everywhere

app/pods/about/route.js

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+import Ember from 'ember';
+import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
+
+export default Ember.Route.extend(AuthenticatedRouteMixin);

app/pods/about/template.hbs

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+<div class="about">
+  <p>This is some information about hymenobacter.info</p>
+</div>

app/pods/application/adapter.js

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+import DS from 'ember-data';
+import Ember from 'ember';
+import config from '../../config/environment';
+
+export default DS.RESTAdapter.extend({
+  namespace: 'api/' + config.genus,
+  host: config.apiURL,
+  coalesceFindRequests: true,
+  ajaxError: function(jqXHR) {
+    // http://stackoverflow.com/a/24027443
+    var error = this._super(jqXHR);
+    if (jqXHR && jqXHR.status === 422) {
+      var response = Ember.$.parseJSON(jqXHR.responseText),
+        errors = {};
+      if (response.errors !== undefined) {
+        var jsonErrors = response.errors;
+        Ember.EnumerableUtils.forEach(Ember.keys(jsonErrors), function(key) {
+          errors[Ember.String.camelize(key)] = jsonErrors[key];
+        });
+      }
+      return new DS.InvalidError(errors);
+    } else {
+      return error;
+    }
+  }
+});

app/pods/application/route.js

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+import Ember from 'ember';
+import ApplicationRouteMixin from 'simple-auth/mixins/application-route-mixin';
+/* global NProgress */
+
+export default Ember.Route.extend(ApplicationRouteMixin, {
+  actions: {
+    loading: function() {
+      NProgress.start();
+      this.router.one('didTransition', function() {
+        return setTimeout((function() {
+          return NProgress.done();
+        }), 50);
+      });
+      return true;
+    }
+  }
+});

app/pods/application/template.hbs

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+  <div class="flakes-navigation">
+    {{#link-to 'index' class='logo'}}
+      <img src="img/logo.png" width="120">
+    {{/link-to}}
+    {{#if session.isAuthenticated}}
+      <ul>
+        {{#link-to 'species' tagName='li' href=false}}
+          {{#link-to 'species'}}Species{{/link-to}}
+        {{/link-to}}
+        {{#link-to 'strains' tagName='li' href=false}}
+          {{#link-to 'strains'}}Strains{{/link-to}}
+        {{/link-to}}
+        {{#link-to 'characteristics' tagName='li' href=false}}
+          {{#link-to 'characteristics'}}Characteristics{{/link-to}}
+        {{/link-to}}
+        {{#link-to 'about' tagName='li' href=false}}
+          {{#link-to 'about'}}About{{/link-to}}
+        {{/link-to}}
+      </ul>
+      <p class="foot">
+        {{session.currentUser.name}}<br>
+        <a {{ action 'invalidateSession' }}>Logout</a>
+      </p>
+    {{else}}
+      <p class="foot">
+        {{#link-to 'login' Login}}Login{{/link-to}}
+        <br>
+        Sign Up
+      </p>
+    {{/if}}
+  </div>
+
+  <div class="flakes-content">
+    <div class="flakes-mobile-top-bar">
+      <a href="" class="logo-wrap">
+        <img src="img/logo.png" height="30px">
+      </a>
+      <a href="" class="navigation-expand-target">
+        <img src="img/navigation-expand-target.png" height="26px">
+      </a>
+    </div>
+
+    <div class="view-wrap">
+      {{outlet}}
+    </div>
+  </div>

app/pods/application/view.js

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

app/pods/characteristics/controller.js

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+import SortableController from '../../controllers/sortable';
+
+export default SortableController.extend({
+  sortBy: 'characteristicName',
+});

app/pods/characteristics/route.js

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

app/pods/characteristics/template.hbs

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+<h2>{{genus-name}} Characteristics</h2>
+<h3>Total characteristics: {{controller.length}}</h3>
+
+<table class="flakes-table">
+  <thead>
+    <tr>
+      <th {{action "setSortBy" "characteristicName"}}>Name</th>
+      <th {{action "setSortBy" "characteristicType"}}>Type</th>
+    </tr>
+  </thead>
+  <tbody>
+    {{#each characteristic in controller}}
+      <tr>
+        <td>{{characteristic.characteristicName}}</td>
+        <td>{{characteristic.characteristicType}}</td>
+      </tr>
+    {{/each}}
+  </tbody>
+</table>

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

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+{{#each error in a}}
+  <div class="flakes-message error">{{error.message}}</div>
+{{/each}}

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

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+import Ember from 'ember';
+import config from '../../../config/environment';
+
+export default Ember.Component.extend({
+  tagName: 'em',
+  genus: config.genus.capitalize(),
+});

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

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+{{genus}}

app/pods/components/measurement-row/component.js

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+import Ember from 'ember';
+
+export default Ember.Component.extend({
+  tagName: 'tr',
+  measurement: null, // passed in
+});

app/pods/components/measurement-row/template.hbs

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+<td>{{measurement.characteristic}}</td>
+<td>{{measurement.computedType}}</td>
+<td>{{{measurement.computedValue}}}</td>
+<td>{{measurement.notes}}</td>
+<td>{{measurement.testMethod}}</td>

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

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+import Ember from 'ember';
+
+export default Ember.Component.extend({
+  tagName: 'span',
+  strain: null, // passed in
+});

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

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+<em>{{strain.species.speciesName}}</em> (strain {{strain.strainName}})

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

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+import Ember from 'ember';
+
+export default Ember.Component.extend({
+  classNames: ['grid-1'],
+  isEditing: false,
+  actions: {
+    save: function() {
+      this.sendAction('save');
+    },
+    cancel: function() {
+      this.sendAction('cancel');
+    },
+  }
+});

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

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+<div class="span-1">
+  <fieldset {{bind-attr class=":flakes-information-box isEditing"}}>
+    <legend>
+      Species
+        {{#if isEditing}}
+          {{input value=species.speciesName}}
+        {{else}}
+          {{species.speciesName}}
+        {{/if}}
+        {{display-errors a=species.errors.speciesName}}
+    </legend>
+
+    {{! ROW 1 }}
+    <div class="grid-4">
+      <dl class="span-2">
+        <dt>Strains</dt>
+        <dd>
+          {{#each species.strains as |strain index|}}
+            {{if index ","}}
+            {{#link-to 'strains.show' strain.id}}
+              {{strain.strainName}}
+            {{/link-to}}
+          {{/each}}
+          {{#if (can "edit species" species)}}
+            {{#if species.isNew}}
+              PENDING SAVE
+            {{else}}
+              <br>
+              {{#link-to 'strains.new' class="button-gray smaller"}}
+                Add Strain
+              {{/link-to}}
+            {{/if}}
+          {{/if}}
+        </dd>
+      </dl>
+      <dl class="span-2">
+        <dt>Type Species?</dt>
+        <dd>
+          {{#if isEditing}}
+            {{input type="checkbox" checked=species.typeSpecies}}
+          {{/if}}
+          {{if species.typeSpecies 'Yes' 'No'}}
+          {{display-errors a=species.errors.typeSpecies}}
+        </dd>
+      </dl>
+    </div>
+
+    {{! ROW 2 }}
+    <div class="grid-4">
+      <dl class="span-4">
+        <dt>Etymology</dt>
+        <dd>
+          {{#if isEditing}}
+            {{textarea value=species.etymology cols="70" rows="3"}}
+          {{else}}
+            {{species.etymology}}
+          {{/if}}
+          {{display-errors a=species.errors.etymology}}
+        </dd>
+      </dl>
+    </div>
+
+    {{! ROW 3 }}
+    <div class="grid-4">
+      <dl class="span-1">
+        <dt>Record Created</dt>
+        <dd>{{null-time species.createdAt 'LL'}}</dd>
+      </dl>
+      <dl class="span-1">
+        <dt>Record Updated</dt>
+        <dd>{{null-time species.updatedAt 'LL'}}</dd>
+      </dl>
+      <dl class="span-1">
+        <dt>Record Deleted</dt>
+        <dd>{{null-time species.deletedAt 'LL'}}</dd>
+      </dl>
+      <dl class="span-1"></dl>
+    </div>
+
+    {{! ROW 4 }}
+    {{#if (can "edit species" species)}}
+      <div class="grid-4">
+        <div class="span-1">
+          {{! Does nothing ATM }}
+          <a {{bind-attr class=":smaller 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/strain-details/component.js

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+import Ember from 'ember';
+
+export default Ember.Component.extend({
+  classNames: ['grid-1'],
+  isEditing: false,
+  actions: {
+    save: function() {
+      this.sendAction('save');
+    },
+    cancel: function() {
+      this.sendAction('cancel');
+    },
+  }
+});

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

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+<div class="span-1">
+  <fieldset {{bind-attr class=":flakes-information-box isEditing"}}>
+    <legend>
+      Strain
+        {{#if isEditing}}
+          {{input value=strain.strainName}}
+        {{else}}
+          {{strain.strainName}}
+        {{/if}}
+        {{display-errors a=strain.errors.strainName}}
+    </legend>
+
+    {{! ROW 1 }}
+    <div class="grid-4">
+      <dl class="span-2">
+        <dt>Species</dt>
+        <dd>
+          {{#if isEditing}}
+            {{
+              view "select"
+              content=species
+              optionValuePath="content.id"
+              optionLabelPath="content.speciesName"
+              selection=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-4">
+      <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}}
+            {{strain.genbank}}
+          {{/if}}
+          {{display-errors a=strain.errors.genbank}}
+        </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 (can "edit strain" strain)}}
+      <div class="grid-4">
+        <div class="span-1">
+          {{! Does nothing ATM }}
+          <a {{bind-attr class=":smaller 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/index/route.js

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+import Ember from 'ember';
+import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
+
+export default Ember.Route.extend(AuthenticatedRouteMixin);

app/pods/index/template.hbs

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+Welcome

app/pods/login/controller.js

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+import Ember from 'ember';
+import LoginControllerMixin from 'simple-auth/mixins/login-controller-mixin';
+
+export default Ember.Controller.extend(LoginControllerMixin, {
+  authenticator: 'simple-auth-authenticator:jwt',
+  loading: false,
+  actions: {
+    authenticate: function() {
+      this.set('errorMessage', null);
+      var _this = this;
+      this.set('loading', true);
+      this._super().then(function() {
+        _this.set('loading', false);
+      }, function(error) {
+        _this.set('loading', false);
+        var message = error.error;
+        _this.set('errorMessage', message);
+      });
+    }
+  }
+});

app/pods/login/route.js

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+import Ember from 'ember';
+
+export default Ember.Route.extend({
+  setupController: function(controller) {
+    controller.set('errorMessage', null);
+  }
+});

app/pods/login/template.hbs

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+{{#if loggedIn}}
+  <p>You are already logged in!</p>
+{{else}}
+  {{#if loading}}
+    <div class="spinner">
+      <div class="double-bounce1"></div>
+      <div class="double-bounce2"></div>
+    </div>
+  {{else}}
+    <form {{action "authenticate" on="submit"}}>
+      <h2>Log In</h2>
+        {{input value=identification type="text" placeholder="Email"}}
+        {{input value=password type="password" placeholder="Password"}}
+        {{input class="button-gray" type="submit" value="Log In"}}
+    </form>
+  {{/if}}
+  {{#if errorMessage}}
+    <div class="flakes-message error">{{errorMessage}}</div>
+  {{/if}}
+{{/if}}

app/pods/species/index/controller.js

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+import SortableController from '../../../controllers/sortable';
+
+export default SortableController.extend({
+  sortBy: 'speciesName',
+});

app/pods/species/index/route.js

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

app/pods/species/index/template.hbs

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+<h2>{{genus-name}} Species</h2>
+<h3>Total species: {{controller.length}}</h3>
+
+{{#if (can "add species")}}
+  {{! Does nothing ATM }}
+  {{#link-to 'species.new' class="button-gray smaller"}}
+    Add Species
+  {{/link-to}}
+{{/if}}
+
+<table class="flakes-table">
+  <thead>
+    <tr>
+      <th {{action "setSortBy" "speciesName"}}>Name</th>
+      <th {{action "setSortBy" "totalStrains"}}>Strains</th>
+    </tr>
+  </thead>
+  <tbody>
+    {{#each species in controller}}
+      <tr>
+        <td>
+          {{#link-to 'species.show' species}}
+            {{species.speciesName}}
+          {{/link-to}}
+        </td>
+        <td>
+          {{#each species.strains as |strain index|}}
+            {{if index ","}}
+            {{#link-to 'strains.show' strain.id}}
+              {{strain.strainName}}
+            {{/link-to}}
+          {{/each}}
+        </td>
+      </tr>
+    {{/each}}
+  </tbody>
+</table>

app/pods/species/new/controller.js

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+import Ember from 'ember';
+
+export default Ember.Controller.extend({
+  isEditing: true,
+  actions: {
+    save: function() {
+      var species = this.get('model');
+      if (species.get('isDirty')) {
+        species.save();
+      }
+      this.transitionToRoute('species.index');
+    },
+    cancel: function() {
+      var species = this.get('model');
+      if (species.get('isNew')) {
+        species.deleteRecord();
+      }
+      this.transitionToRoute('species.index');
+    }
+  }
+});

app/pods/species/new/route.js

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+import Ember from 'ember';
+
+export default Ember.Route.extend({
+  model: function() {
+    return this.store.createRecord('species');
+  },
+  actions: {
+    cancelSpecies: function() {
+      this.transitionTo('species.index');
+    }
+  }
+});

app/pods/species/new/template.hbs

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+{{
+  species-details
+  species=model
+  isEditing=true
+  save="save"
+  cancel="cancel"
+}}

app/pods/species/show/controller.js

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

app/pods/species/show/route.js

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+import Ember from 'ember';
+
+export default Ember.Route.extend({
+});

app/pods/species/show/template.hbs

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+{{
+  species-details
+  species=model
+  isEditing=isEditing
+  save="save"
+  cancel="cancel"
+}}

app/pods/strains/index/route.js

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

app/pods/strains/index/template.hbs

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+<h2>{{genus-name}} Strains</h2>
+<h3>Total strains: {{controller.length}}</h3>
+
+{{#if (can "add strain")}}
+  {{! Does nothing ATM }}
+  {{#link-to 'strains.new' class="button-gray smaller"}}
+    Add Strain
+  {{/link-to}}
+{{/if}}
+
+<table class="flakes-table">
+  <thead>
+    <tr>
+      <th {{action "setSortBy" "fullName"}}>Name</th>
+      <th {{action "setSortBy" "totalMeasurements"}}>Total Measurements</th>
+    </tr>
+  </thead>
+  <tbody>
+    {{#each strain in controller}}
+      <tr>
+        <td>
+          {{#link-to 'strains.show' strain.id}}
+            {{scientific-name strain=strain}}
+          {{/link-to}}
+        </td>
+        <td>{{strain.totalMeasurements}}</td>
+      </tr>
+    {{/each}}
+  </tbody>
+</table>

app/pods/strains/new/controller.js

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+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

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+import Ember from 'ember';
+
+export default Ember.Route.extend({
+  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/new/template.hbs

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+{{
+  strain-details
+  strain=strain
+  species=species
+  isEditing=true
+  save="save"
+  cancel="cancel"
+}}

app/pods/strains/show/controller.js

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+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/strains/show/route.js

@@ -0,0 +1,13 @@
+import Ember from 'ember';
+
+export default Ember.Route.extend({
+  model: function(params) {
+    return Ember.RSVP.hash({
+      strain: this.store.find('strain', params.strain_id),
+      species: this.store.findAll('species')
+    });
+  },
+  setupController: function(controller, models) {
+    controller.setProperties(models);
+  },
+});

app/pods/strains/show/template.hbs

@@ -0,0 +1,8 @@
+{{
+  strain-details
+  strain=strain
+  species=species
+  isEditing=isEditing
+  save="save"
+  cancel="cancel"
+}}

app/pods/user/adapter.js

@@ -0,0 +1,8 @@
+import DS from 'ember-data';
+import config from '../../config/environment';
+
+export default DS.RESTAdapter.extend({
+  namespace: 'api',
+  host: config.apiURL,
+  coalesceFindRequests: true,
+});

app/pods/users/route.js

@@ -0,0 +1,8 @@
+import Ember from 'ember';
+import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
+
+export default Ember.Route.extend(AuthenticatedRouteMixin, {
+  model: function() {
+    return this.store.findAll('user');
+  }
+});

app/pods/users/template.hbs

@@ -0,0 +1,3 @@
+{{#each user in model}}
+  {{user.email}}<br>
+{{/each}}