Merge pull request #150 from Duke-GCB/138-file-picker-handle-single-f…

…ile-array

Simple support for workflows using FASTQReadPairType[]

app/components/questionnaire/fastq-file-pair-list.js

@@ -1,8 +1,10 @@
 import Ember from 'ember';
 import FileGroupList from 'bespin-ui/components/questionnaire/file-group-list';
 import { FASTQFileItemList } from 'bespin-ui/utils/fastq-file-item-list';
+import layout from 'bespin-ui/templates/components/questionnaire/fastq-file-pair-list';
 
 const FASTQFilePairList = FileGroupList.extend({
+  layout, // https://github.com/emberjs/rfcs/issues/412#issuecomment-423499140
   groupSize: 2,
   answerFormErrors: null,
   fieldErrors: Ember.computed('answerFormErrors.errors.[]', 'fieldName', function() {

app/components/questionnaire/fastq-read-pair-list.js

@@ -0,0 +1,26 @@
+import Ember from 'ember';
+import FASTQFilePairList from './fastq-file-pair-list';
+
+export default FASTQFilePairList.extend({
+  // Primary purpose of this subclass is to provide a different structure from the 'answer'
+  // method that returns single files wrapped in an array.
+  answer: Ember.computed('fieldName', 'fileItems.cwlObjectValue.[]', function() {
+    const fieldName = this.get('fieldName');
+    // Convert NamedFASTQFilePairType to a FASTQReadPairType
+    const fastqReadPairs = this.get('fileItems.cwlObjectValue').map(namedPair => {
+      return Ember.Object.create({
+        name: namedPair.get('name'),
+        read1_files: [namedPair.get('file1')],
+        read2_files: [namedPair.get('file2')]
+      });
+    });
+
+    const answer = Ember.Object.create();
+    answer.set(fieldName, fastqReadPairs);
+    return answer;
+  }),
+  // Support Message
+  featureSupportMessage: Ember.String.htmlSafe('<strong>Note:</strong> This workflow supports multiple file pairs per read. ' +
+    'However, the web interface only supports choosing one file pair per read. If you wish to run this workflow with multiple files per ' +
+    'read, please use <a href="https://github.com/Duke-GCB/bespin-cli">bespin-cli</a>.'),
+});

app/components/questionnaire/file-group-list.js

@@ -53,6 +53,9 @@ const FileGroupList = DDSProjectField.extend({
     }
   },
 
+  // Message to display if additional functionality is available elsewhere (e.g. CLI)
+  featureSupportMessage: null,
+
   init() {
     this._super(...arguments);
     if(Ember.isEmpty(this.get('fileItems'))) {

app/templates/components/questionnaire/fastq-file-pair-list.hbs

@@ -4,6 +4,11 @@
 </div>
 <div class="col-md-6 file-group-list-selections">
   <label>Selected {{ groupTitle }} {{ groupSizeName }}</label>
+  {{#if featureSupportMessage}}
+    <div class="feature-support-message alert alert-warning">
+      {{featureSupportMessage}}
+    </div>
+  {{/if}}
   {{#each samples as |pair pairIndex|}}
     {{questionnaire/fastq-file-pair-row pair pairIndex (action 'removeAt')}}
   {{else}}

app/utils/component-settings.js

@@ -28,6 +28,20 @@ const ComponentSettings = [
       }
     ]
   },
+  {
+    // Bespin CWL FASTQReadPairType - pair of arrays
+    // We support a basic version of this, providing a single file in each array
+    cwlType: { type: 'array', items: 'FASTQReadPairType'}, // Named in job-questionnaire.user_fields_json
+    name: 'fastq-read-pair-list',  // questionnaire component to render
+    formats: [
+      {
+        title: 'FASTQ Pair',
+        format: null, // The specific files should be http://edamontology.org/format_1930, but this is a structure
+        fileNameRegexStr: '.*(fq$)|(fq.gz$)|(fastq$)|(fastq.gz$)',
+        groupName: 'Sample'
+      }
+    ]
+  },
   {
     // String field
     cwlType: 'string', // Named in job-questionnaire.user_fields_json

tests/integration/components/questionnaire/fastq-file-pair-list-test.js

@@ -59,3 +59,14 @@ test('it correctly observes error array', function(assert) {
     assert.equal(this.$('.error-panel').text().trim(), 'Incomplete');
   });
 });
+
+test('it shows no featureSupportMessage', function(assert) {
+  const fileItems = Ember.Object.create({
+      samples: [{},{}]
+    }
+  );
+  this.set('fileItems', fileItems);
+  this.set('externalAction', () => {});
+  this.render(hbs`{{questionnaire/fastq-file-pair-list "FieldName" (action externalAction) fileItems=fileItems}}`);
+  assert.equal(this.$('.feature-support-message').length, 0);
+});

tests/integration/components/questionnaire/fastq-read-pair-list-test.js

@@ -0,0 +1,35 @@
+import { moduleForComponent, test } from 'ember-qunit';
+import hbs from 'htmlbars-inline-precompile';
+import StoreStub from '../../../helpers/store-stub';
+import Ember from 'ember';
+
+moduleForComponent('questionnaire/fastq-read-pair-list', 'Integration | Component | questionnaire/fastq read pair list', {
+  integration: true,
+  beforeEach: function() {
+    this.register('service:store', StoreStub);
+  }
+});
+
+test('it renders using the fastq-file-pair-list template', function(assert) {
+  const fileItems = Ember.Object.create({
+      samples: [{},{}]
+    }
+  );
+  this.set('fileItems', fileItems);
+  this.set('externalAction', () => {});
+  this.render(hbs`{{questionnaire/fastq-read-pair-list "FieldName" (action externalAction) fileItems=fileItems}}`);
+  assert.equal(this.$('.fastq-file-pair-row').length, 2);
+  assert.equal(this.$('div.file-group-list-picker').length, 1);
+
+});
+
+test('It shows the featureSupportMessage', function(assert) {
+  const fileItems = Ember.Object.create({
+      samples: [{},{}]
+    }
+  );
+  this.set('fileItems', fileItems);
+  this.set('externalAction', () => {});
+  this.render(hbs`{{questionnaire/fastq-read-pair-list "FieldName" (action externalAction) fileItems=fileItems}}`);
+  assert.equal(this.$('.feature-support-message').length, 1);
+});

tests/unit/components/questionnaire/fastq-file-pair-list-test.js

@@ -131,3 +131,9 @@ test('it requires fieldName and answerChanged', function(assert) {
   });
   this.subject({fieldName: "SomeField", answerChanged: ()=>{}});
 });
+
+test('it has no featureSupportMessage', function(assert) {
+  const fastqFilePairList = this.subject({fieldName: "SomeField", answerChanged: ()=>{}});
+  const message = fastqFilePairList.get('featureSupportMessage');
+  assert.notOk(message);
+});

tests/unit/components/questionnaire/fastq-read-pair-list-test.js

@@ -0,0 +1,35 @@
+import { moduleForComponent, test } from 'ember-qunit';
+import Ember from 'ember';
+
+moduleForComponent('questionnaire/fastq-read-pair-list', 'Unit | Component | questionnaire/fastq read pair list', {
+  // Specify the other units that are required for this test
+  needs: ['service:dds-projects', 'service:dds-user-credentials'],
+  unit: true
+});
+
+test('it computes answer with field name and files', function (assert) {
+
+  const expected = Ember.Object.create({read_pairs: [{name: 'abc', read1_files: [{class: 'File', path: 'abc_1'}], read2_files: [{class: 'File', path: 'abc_2'}]}]});
+  const fieldName = 'read_pairs';
+  const mockFileItems = Ember.Object.create({
+    cwlObjectValue: [
+      Ember.Object.create({name: 'abc', file1: {class: 'File', path: 'abc_1'}, file2: {class: 'File', path: 'abc_2'}})
+    ]
+  });
+
+  const fastqReadPairList = this.subject({
+    groupSize: 2,
+    fileItems: mockFileItems,
+    fieldName: fieldName,
+    answerChanged: () => {
+    }
+  });
+  const answer = fastqReadPairList.get('answer');
+  assert.equal(JSON.stringify(answer), JSON.stringify(expected));
+});
+
+test('it provides feature support message with link to bespin-cli', function(assert) {
+  const fastqReadPairList = this.subject({fieldName: "SomeField", answerChanged: ()=>{}});
+  const messageString = fastqReadPairList.get('featureSupportMessage.string');
+  assert.ok(messageString.indexOf('https://github.com/Duke-GCB/bespin-cli') > 0);
+});