Inline /contigs and /spec calls

cycledash/static/js/examine/RecordStore.js

@@ -27,9 +27,10 @@ var ENTIRE_GENOME = {start: null, end: null, contig: types.ALL_CHROMOSOMES};
 
 // opt_testDataSource is provided for testing.
 // Its type is function(url, done_callback).
-function createRecordStore(vcfId, dispatcher, opt_testDataSource) {
+function createRecordStore(run, dispatcher, opt_testDataSource) {
   // Initial state of the store. This is mutable. There be monsters.
-  var hasLoaded = false,
+  var vcfId = run.id,
+      hasLoaded = false,
       loadError = null,
 
       records = [],
@@ -41,8 +42,8 @@ function createRecordStore(vcfId, dispatcher, opt_testDataSource) {
       sortBys = DEFAULT_SORT_BYS,
       range = ENTIRE_GENOME,
 
-      contigs = [],
-      columns = {};
+      contigs = run.contigs,
+      columns = run.spec;
 
   // State for paging the server for records. Page should be reset to 0 on most
   // operations.
@@ -120,6 +121,7 @@ function createRecordStore(vcfId, dispatcher, opt_testDataSource) {
 
     $.when(deferredGenotypes(vcfId, query))
       .done(response => {
+        hasLoaded = true;
         if (append) {
           // TODO: BUG: This can result in a out-of-order records, if a later
           //            XHR returns before an earlier XHR.
@@ -219,42 +221,23 @@ function createRecordStore(vcfId, dispatcher, opt_testDataSource) {
     range = query.range || ENTIRE_GENOME;
   }
 
-  // Initialize the RecordStore with basic information (columns, the contigs
-  // in the VCF), and request first records to display.
-  $.when(deferredSpec(vcfId), deferredContigs(vcfId))
-    .done((columnsResponse, contigsResponse) => {
-      hasLoaded = true;
-      columns = columnsResponse.spec;
-      contigs = contigsResponse.contigs;
-
-      var existingQuery = getQueryStringValue('query');
-      if (existingQuery) {
-        try {
-          var jsonQuery = JSON.parse(existingQuery);
-          setQuery(jsonQuery);
-        } catch (e) {
-          // query is invalid
-        }
-      }
+  var existingQuery = getQueryStringValue('query');
+  if (existingQuery) {
+    try {
+      var jsonQuery = JSON.parse(existingQuery);
+      setQuery(jsonQuery);
+    } catch (e) {
+      // query is invalid
+    }
+  }
 
-      // no need to debounce this update -- make it so now!
-      _updateGenotypes({append: false});
-    });
+  // no need to debounce this update -- make it so now!
+  _updateGenotypes({append: false});
 
   function notifyChange() {
     _.each(listenerCallbacks, cb => { cb(); });
   }
 
-  // Return deferred GET for the column spec for a given VCF.
-  function deferredSpec(vcfId) {
-    return callbackToPromise(dataSource, '/runs/' + vcfId + '/spec');
-  }
-
-  // Return deferred GET for the contigs in a given VCF.
-  function deferredContigs(vcfId) {
-    return callbackToPromise(dataSource, '/runs/' + vcfId + '/contigs');
-  }
-
   // Return a deferred GET returning genotypes and stats.
   function deferredGenotypes(vcfId, query) {
     var queryString = encodeURIComponent(JSON.stringify(query));

cycledash/static/js/examine/components/QueryBox.js

@@ -51,12 +51,10 @@ var QueryBox = React.createClass({
       this.props.handleQueryChange(parsedQuery);
     }
   },
+  componentDidMount: function(prevProps, prevState) {
+    this.initQueryBox();
+  },
   componentDidUpdate: function(prevProps, prevState) {
-    // Watch for the first update with a populated set of columns.
-    if (_.isEmpty(prevProps.columns) && !_.isEmpty(this.props.columns)) {
-      this.initQueryBox();
-    }
-
     if (prevProps.query != this.props.query) {
       this.setQueryBoxToQuery();
     }

cycledash/static/js/examine/examine.js

@@ -10,7 +10,7 @@ var React = require('react'),
 window.renderExaminePage = function(el, run, igvHttpfsUrl) {
   var dispatcher = new Dispatcher();
   var recordActions = getRecordActions(dispatcher);
-  var recordStore = createRecordStore(run.id, dispatcher);
+  var recordStore = createRecordStore(run, dispatcher);
   React.render(<ExaminePage recordStore={recordStore}
                             recordActions={recordActions}
                             run={run}

cycledash/views.py

@@ -86,22 +86,15 @@ def genotypes(run_id):
     return jsonify(gt.get(run_id, json.loads(request.args.get('q'))))
 
 
-@app.route('/runs/<run_id>/spec')
-def examine_spec(run_id):
-    return jsonify({'spec': gt.spec(run_id)})
-
-
-@app.route('/runs/<run_id>/contigs')
-def contigs(run_id):
-    return jsonify({'contigs': gt.contigs(run_id)})
-
-
 @app.route('/runs/<run_id>/examine')
 def examine(run_id):
     with db.engine.connect() as con:
         select_vcf_sql = 'select * from vcfs where id = {};'.format(run_id)
         vcf = dict(con.execute(select_vcf_sql).fetchall()[0])
-    return render_template('examine.html', run=dict(vcf))
+    run = dict(vcf)
+    run['spec'] = gt.spec(run_id)
+    run['contigs'] = gt.contigs(run_id)
+    return render_template('examine.html', run=run)
 
 
 @app.route('/runs/<run_ids_key>/concordance', methods=['GET', 'PUT'])

tests/js/DataUtils-test.js

@@ -6,7 +6,7 @@ var dataUtils = require('./DataUtils'),
     vcf = require('vcf.js'),
     _ = require('underscore');
 
-describe('test data', function() {
+describe('DataUtils', function() {
   var vcfData;
   before(function() {
     var parseVcf = vcf.parser();  // Note: the real deal, not a fake!
@@ -19,7 +19,7 @@ describe('test data', function() {
   });
 
   it('should generate a column spec', function() {
-    var spec = dataUtils.getSpec(vcfData).spec;
+    var spec = dataUtils.getSpec(vcfData);
     assert.deepEqual(['INFO', 'SAMPLE'], _.keys(spec));
     assert.deepEqual(['DP','SOMATIC','SS','SSC','GPV','SPV'], _.keys(spec.INFO));
     assert.deepEqual(['GT','GQ','DP','RD','AD','FREQ','DP4'], _.keys(spec.SAMPLE));

tests/js/DataUtils.js

@@ -34,15 +34,15 @@ function getSpec(vcfData) {
 
   // TODO: add sample_name
 
-  return {spec: cols};
+  return cols;
 }
 
 function getContigs(vcfData) {
   return _.uniq(vcfData.records.map(rec => rec.CHROM));
 }
 
 function getRecords(vcfData) {
-  var spec = getSpec(vcfData).spec;
+  var spec = getSpec(vcfData);
   return _.flatten(vcfData.records.map((record) => {
     var baseProps = {
       contig: record.CHROM,
@@ -81,11 +81,7 @@ function makeFakeServer(vcfPath) {
 
   var genotypesUrl = '/runs/1/genotypes';
   var get = function(path, callback) {
-    if (path == '/runs/1/spec') {
-      callback(spec);
-    } else if (path == '/runs/1/contigs') {
-      callback({contigs: contigs});
-    } else if (path.slice(0, genotypesUrl.length) == genotypesUrl) {
+    if (path.slice(0, genotypesUrl.length) == genotypesUrl) {
       callback({
         records: records,
         stats: {
@@ -94,7 +90,7 @@ function makeFakeServer(vcfPath) {
         }
       });
     } else {
-      throw new Error('Unexpected request');
+      throw new Error('Unexpected request for ' + path);
     }
   };
 

tests/js/ExaminePage-test.js

@@ -38,16 +38,19 @@ describe('ExaminePage', function() {
   });
 
   it('should display and select records', function() {
-    var dispatcher = new Dispatcher();
-    var recordActions = RecordActions.getRecordActions(dispatcher);
-    var recordStore = createRecordStore(1, dispatcher, fakeServer);
     var run = {
       id: 1,
+      spec: fakeServer.spec,
+      contigs: fakeServer.contigs,
       caller_name: 'test',
       dataset_name: 'test',
       created_at: '',
       uri: '/tests/js/data/snv.vcf'
     };
+
+    var dispatcher = new Dispatcher();
+    var recordActions = RecordActions.getRecordActions(dispatcher);
+    var recordStore = createRecordStore(run, dispatcher, fakeServer);
     var examine = TestUtils.renderIntoDocument(
       <ExaminePage recordStore={recordStore}
                    recordActions={recordActions}

tests/js/Utils.js

@@ -14,15 +14,13 @@ function findInComponent(selector, component) {
   return _.toArray(component.getDOMNode().querySelectorAll(selector));
 }
 
-
 /**
- * Stub out a React class method using Sinon.
+ * Stub out a React class method with the given function using Sinon.
  * Returns the Sinon stub. Don't forget to call .restore() on it!
  */
 function stubReactMethod(ReactClass, method, fn) {
   return sinon.stub(ReactClass.type.prototype.__reactAutoBindMap, method, fn);
-};
-
+}
 
 function makeObj(list, keyValFn) {
   return _.object(list.map(keyValFn));