update merge from master

app/pods/protected/about/route.js

@@ -0,0 +1,4 @@
+import Ember from 'ember';
+import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
+
+export default Ember.Route.extend(AuthenticatedRouteMixin);

app/pods/protected/about/template.hbs

@@ -0,0 +1,3 @@
+<div class="about">
+  <p>This is some information about clostridium.info</p>
+</div>

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

@@ -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() {
+    return this.store.findAll('characteristic');
+  },
+
+});

app/pods/protected/characteristics/template.hbs

@@ -0,0 +1,21 @@
+<h2>{{genus-name}} Characteristics</h2>
+<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.characteristicTypeName}}</td>
+        <td>{{row.sortOrder}}</td>
+      </tr>
+    {{/each}}
+  </tbody>
+</table>

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

@@ -0,0 +1,26 @@
+<div class="overflow-div">
+  <table class="flakes-table">
+    <thead>
+      <tr>
+        <th>Characteristic</th>
+        {{#each strains as |strain|}}
+          <th>
+            {{#link-to 'protected.strains.show' strain.id classBinding="data.typeStrain:type-strain"}}
+              {{strain.fullNameMU}}
+            {{/link-to}}
+          </th>
+        {{/each}}
+      </tr>
+    </thead>
+    <tbody>
+      {{#each data as |row|}}
+        <tr>
+          <td>{{row.characteristic}}</td>
+          {{#each strains as |strain|}}
+            <td>{{get-property row strain.id}}</td>
+          {{/each}}
+        </tr>
+      {{/each}}
+    </tbody>
+  </table>
+</div>

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

@@ -0,0 +1,41 @@
+<h2>{{genus-name}} - Compare Strains</h2>
+
+<div class="span-1">
+  <fieldset>
+    <form>
+      <ul>
+        <li>
+          <label>Strains</label>
+          {{
+            select-2
+            multiple=true
+            content=strains
+            value=selectedStrains
+            optionValuePath="id"
+            optionLabelPath="fullNameMU"
+            placeholder="Select one or more strains"
+          }}
+        </li>
+        <li>
+          <label>Characteristics</label>
+          {{
+            select-2
+            multiple=true
+            content=characteristics
+            value=selectedCharacteristics
+            optionValuePath="id"
+            optionLabelPath="characteristicName"
+            placeholder="Select one or more characteristics"
+          }}
+        </li>
+        <li>
+          <a class="action button-gray smaller right" {{action 'search'}}>
+            Search
+          </a>
+        </li>
+      </ul>
+    </form>
+  </fieldset>
+</div>
+
+{{outlet}}

app/pods/protected/index/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, {
+  beforeModel: function(transition) {
+    this._super(transition);
+    this.transitionTo('protected.compare');
+  }
+});

app/pods/protected/index/template.hbs

@@ -0,0 +1 @@
+Welcome

app/pods/protected/measurements/route.js

@@ -0,0 +1,4 @@
+import Ember from 'ember';
+import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
+
+export default Ember.Route.extend(AuthenticatedRouteMixin, {});

app/pods/protected/measurements/template.hbs

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

app/pods/protected/route.js

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+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() {
+    let token = this.get('session.secure.token');
+    let user = parseBase64(token);
+    return this.store.find('user', user.sub);
+  },
+
+});

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/edit/template.hbs

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

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

@@ -0,0 +1,34 @@
+<h2>{{genus-name}} Species</h2>
+<h3>Total species: {{model.length}}</h3>
+
+{{add-button label="Add Species" link="protected.species.new" canAdd=metaData.canAdd}}
+
+<table class="flakes-table">
+  <thead>
+    <tr>
+      <th>Name</th>
+      <th>Strains</th>
+    </tr>
+  </thead>
+  <tbody>
+    {{#each sortedSpecies as |species|}}
+      <tr>
+        <td>
+          <em>
+            {{#link-to 'protected.species.show' species}}
+              {{species.speciesName}}
+            {{/link-to}}
+          </em>
+        </td>
+        <td>
+          {{#each species.strains as |strain index|}}
+            {{if index ","}}
+            {{#link-to 'protected.strains.show' strain.id}}
+              {{{strain.strainNameMU}}}
+            {{/link-to}}
+          {{/each}}
+        </td>
+      </tr>
+    {{/each}}
+  </tbody>
+</table>

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

@@ -0,0 +1,65 @@
+<div class="grid-1">
+  <div class="span-1">
+    <fieldset class="flakes-information-box {{if isEditing 'is-editing'}}">
+      <legend>
+        Species <em>{{model.speciesName}}</em>
+      </legend>
+
+      {{! ROW 1 }}
+      <div class="grid-2 gutter-20">
+        <dl class="span-1">
+          <dt>Strains</dt>
+          <dd>
+            <ul>
+              {{#each model.strains as |strain index|}}
+                <li>
+                  {{#link-to 'protected.strains.show' strain.id}}
+                    {{{strain.strainNameMU}}}
+                  {{/link-to}}
+                </li>
+              {{/each}}
+            </ul>
+          </dd>
+        </dl>
+        <dl class="span-1">
+          <dt>Type Species?</dt>
+          <dd>
+            {{if model.typeSpecies 'Yes' 'No'}}
+          </dd>
+        </dl>
+      </div>
+
+      {{! ROW 2 }}
+      <div class="grid-1 gutter-20">
+        <dl class="span-1">
+          <dt>Etymology</dt>
+          <dd>
+            {{model.etymology}}
+          </dd>
+        </dl>
+      </div>
+
+      {{! ROW 3 }}
+      <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>
+</div>
+{{#if model.canEdit}}
+  <br>
+  {{#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

@@ -0,0 +1,22 @@
+import Ember from 'ember';
+import AuthenticatedRouteMixin from 'simple-auth/mixins/authenticated-route-mixin';
+
+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'), // 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

@@ -0,0 +1,7 @@
+{{
+  forms/strain-form
+  strain=strain
+  species=species
+  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

@@ -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('strain');
+  },
+});

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

@@ -0,0 +1,27 @@
+<h2>{{genus-name}} Strains</h2>
+<h3>Total strains: {{model.length}}</h3>
+
+{{add-button label="Add Strain" link="protected.strains.new" canAdd=metaData.canAdd}}
+
+<table class="flakes-table">
+  <thead>
+    <tr>
+      <th>Species</th>
+      <th>Total Measurements</th>
+    </tr>
+  </thead>
+  <tbody>
+    {{#each sortedStrains as |row|}}
+      <tr>
+        <td>
+          {{#link-to 'protected.strains.show' row.id classBinding="data.typeStrain:type-strain"}}
+            {{row.fullNameMU}}
+          {{/link-to}}
+        </td>
+        <td>
+          {{row.totalMeasurements}}
+        </td>
+      </tr>
+    {{/each}}
+  </tbody>
+</table>

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

@@ -0,0 +1,7 @@
+{{
+  forms/strain-form
+  strain=strain
+  species=species
+  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}}