MAINT: Read-only user

Refactor measurements

.gitignore

@@ -15,3 +15,4 @@
 /libpeerconnection.log
 npm-debug.log
 testem.log
+.firebase

app/mixins/delete-model.js

@@ -8,7 +8,10 @@ export default Mixin.create({
   actions: {
     delete: function() {
       this.get('model').destroyRecord().then(() => {
-        this.get('store').unloadAll();
+        // Instead of unloading the entire store, we keep the loaded user models
+        ['species', 'strain', 'characteristic', 'measurement'].map((model) => {
+          this.get('store').unloadAll(model);
+        });
         this.transitionToRoute(this.get('transitionRoute'));
       });
     },

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -1,12 +1,11 @@
 {{#if canAdd}}
   <br>
-  <button class="button-green smaller" {{action "addCharacteristic"}}>
-    Add characteristic
+  <button class="button-green smaller" {{action "addMeasurement"}}>
+    Add measurement
   </button>
   <br><br>
 {{/if}}
 
-{{#if measurementsPresent}}
 {{#if paramsChanged}}
   <button class="button-gray smaller" {{action 'resetSortParam'}}>
     Reset sort
@@ -48,9 +47,10 @@
         allCharacteristics=allCharacteristics
         canEdit=canEdit
       }}
+    {{else}}
+      <tr>
+        <td colspan="5">No Measurements on Record</td>
+      </tr>
     {{/each}}
   </tbody>
 </table>
-{{else}}
-No measurements on record.
-{{/if}}

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

@@ -71,11 +71,11 @@
     {{! ROW 5 }}
     <div class="grid-1 gutter-20">
       <dl class="span-1">
-        <dt>Characteristics</dt>
+        <dt>Characteristic Measurements</dt>
         <dd>
           {{
             protected/strains/measurements-table
-            strain=strain
+            measurements=strain.measurements
             canEdit=false
             canAdd=false
           }}

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

@@ -9,22 +9,22 @@ export default Component.extend(SetupMetaData, {
   isNew: null,
   isDirty: false,
   speciesList: null,
-  allCharacteristics: null,
+  allCharacteristics: [],
+  updateQueue: [],
+  deleteQueue: [],
 
   // Actions
   "on-save": null,
   "on-cancel": null,
   "on-update": null,
-  "add-characteristic": null,
-  "save-measurement": null,
-  "delete-measurement": null,
+  "add-measurements": null,
 
   // CPs
   sortParams: ['sortOrder'],
   sortedSpeciesList: sort('speciesList', 'sortParams'),
 
   // Property mapping
-  propertiesList: ['strainName', 'typeStrain', 'species', 'isolatedFrom', 'accessionNumbers', 'genbank', 'wholeGenomeSequence', 'notes'],
+  propertiesList: ['strainName', 'typeStrain', 'species', 'isolatedFrom', 'accessionNumbers', 'genbank', 'wholeGenomeSequence', 'notes', 'measurements'],
   strainName: null,
   typeStrain: null,
   species: null,
@@ -33,15 +33,55 @@ export default Component.extend(SetupMetaData, {
   genbank: null,
   wholeGenomeSequence: null,
   notes: null,
+  measurements: [],
+
+  // Dropdown menu
+  characteristics: [],
+  charSortParams: ['characteristicTypeName', 'sortOrder', 'characteristicName'],
+  sortedCharacteristics: sort('characteristics', 'charSortParams'),
+  setupCharacteristics: Ember.on('init', function() {
+    const tempArray = this._resetArray(this.get('allCharacteristics'));
+    this.set('characteristics', tempArray);
+  }),
 
   resetOnInit: Ember.on('init', function() {
+    this._resetProperties();
+  }),
+
+  _resetArray: function(arr) {
+    let tempArray = [];
+    arr.forEach((val) => {
+      if (!val.get('isNew')) {
+        tempArray.push(val);
+      }
+    });
+    return tempArray;
+  },
+
+  _resetProperties: function() {
+    // Still some coupling going on here because of adding strain to measurement
+    this.get('measurements').forEach((val) => {
+      if (val.get('hasDirtyAttributes')) {
+        val.rollbackAttributes();
+      }
+      if (val.get('isNew')) {
+        this.get('strain.measurements').removeObject(val);
+      }
+    });
     this.get('propertiesList').forEach((field) => {
       const valueInStrain = this.get('strain').get(field);
+      if (field === 'measurements') {
+        const tempArray = this._resetArray(valueInStrain);
+        this.set(field, tempArray);
+      } else {
         this.set(field, valueInStrain);
+      }
     });
+    this.set('updateQueue', []);
+    this.set('deleteQueue', []);
     // Read-only attributes
     this.set('isNew', this.get('strain.isNew'));
-  }),
+  },
 
   updateField: function(property, value) {
     this.set(property, value);
@@ -55,23 +95,32 @@ export default Component.extend(SetupMetaData, {
 
   actions: {
     save: function() {
-      return this.attrs['on-save'](this.getProperties(this.get('propertiesList')));
+      return this.attrs['on-save'](this.getProperties(this.get('propertiesList')), this.get('deleteQueue'), this.get('updateQueue'));
     },
 
     cancel: function() {
+      this._resetProperties();
       return this.attrs['on-cancel']();
     },
 
-    addCharacteristic: function() {
-      return this.attrs['add-characteristic']();
+    addMeasurement: function() {
+      const measurement = this.attrs['add-measurement']();
+      this.get('measurements').pushObject(measurement);
     },
 
     saveMeasurement: function(measurement, properties) {
-      return this.attrs['save-measurement'](measurement, properties);
+      measurement.setProperties(properties);
+      measurement.set('strain', this.get('strain'));
+      if (!measurement.get('isNew')) {
+        this.get('updateQueue').pushObject(measurement);
+      }
+      this.set('isDirty', true);
     },
 
     deleteMeasurement: function(measurement) {
-      return this.attrs['delete-measurement'](measurement);
+      this.get('deleteQueue').pushObject(measurement);
+      this.get('measurements').removeObject(measurement);
+      this.set('isDirty', true);
     },
 
     strainNameDidChange: function(value) {
@@ -104,7 +153,7 @@ export default Component.extend(SetupMetaData, {
     },
 
     notesDidChange: function(value) {
-      this.updateField('strain.notes', value);
+      this.updateField('notes', value);
     },
   },
 });

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

@@ -61,9 +61,9 @@
     <div>
       {{
         protected/strains/measurements-table
-        strain=strain
-        add-characteristic=(action "addCharacteristic")
-        allCharacteristics=allCharacteristics
+        measurements=measurements
+        add-measurement=(action "addMeasurement")
+        allCharacteristics=sortedCharacteristics
         save-measurement=(action "saveMeasurement")
         delete-measurement=(action "deleteMeasurement")
         canEdit=strain.canEdit

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

@@ -1,11 +1,11 @@
 import Ember from 'ember';
-import ajaxErrorNew from '../../../../utils/ajax-error-new';
 
 const { Controller, inject: { service } } = Ember;
 
 export default Controller.extend({
   session: service(),
   ajax: service(),
+  ajaxError: service('ajax-error'),
   currentUser: service('session-account'),
 
   actions: {
@@ -15,12 +15,13 @@ export default Controller.extend({
       this.get('ajax').post('/users/password', { data: data }).then(() => {
         this.transitionToRoute('protected.users.show', id);
         this.get('flashMessages').information('Your password has been changed.');
-      }, (error) => {
-        ajaxErrorNew(error, this.get('flashMessages'));
+      }, (errors) => {
+        this.get('ajaxError').alert(errors);
       });
     },
 
     cancel: function() {
+      this.get('flashMessages').clearMessages();
       this.transitionToRoute('protected.users.show', this.get('currentUser.account.id'));
     },
   },

app/serializers/application.js

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

app/services/ajax-error.js

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

app/utils/ajax-error-new.js

@@ -1,7 +0,0 @@
-export default function ajaxErrorNew(error, flash) {
-  flash.clearMessages();
-  error.errors.forEach((error) => {
-    const source = error.source.pointer.split('/');
-    flash.error(`${source[source.length-1].replace(/([A-Z])/g, ' $1').capitalize()} - ${error.detail}`);
-  });
-}

package.json

@@ -10,7 +10,11 @@
   "scripts": {
     "build": "ember build",
     "start": "ember server",
-    "test": "ember test"
+    "test": "ember test",
+    "bower": "bower",
+    "ember": "ember",
+    "firebase": "firebase",
+    "deployProd": "firebase deploy -e prod"
   },
   "repository": "",
   "engines": {
@@ -40,5 +44,9 @@
     "ember-export-application-global": "^1.0.4",
     "ember-one-way-input": "0.1.3",
     "ember-simple-auth": "1.0.1"
+  },
+  "dependencies": {
+    "bower": "^1.8.8",
+    "firebase-tools": "^7.12.1"
   }
 }