Add combobox selection for VCF to validate against

Also start the slow process of renaming run -> vcf.

Add pdiff test (but not the screenshots)

fixes #520

cycledash/genotypes.py

@@ -60,7 +60,7 @@ def contigs(vcf_id):
     return [contig for (contig,) in results]
 
 
-def get(vcf_id, query, with_stats=True, truth_vcf_id=None):
+def get(vcf_id, query, with_stats=True):
     """Return a list of genotypes in a vcf conforming to the given query, as
     well as a dict of stats calculated on them.
 
@@ -84,14 +84,15 @@ def get(vcf_id, query, with_stats=True, truth_vcf_id=None):
     }
     """
     query = _annotate_query_with_types(query, spec(vcf_id))
+    validate_vcf_id = query.get('selectedVcfId')
     with tables(db, 'genotypes') as (con, g):
-        if truth_vcf_id:
+        if validate_vcf_id:
             # We consider a genotype validated if a truth genotype exists at its
             # location (contig/position) with the same ref/alts.  This isn't
             # entirely accurate: for example, it handles SVs very poorly.
             gt = g.alias()
             joined_q = outerjoin(g, gt, and_(
-                gt.c.vcf_id == truth_vcf_id,
+                gt.c.vcf_id == validate_vcf_id,
                 g.c.contig == gt.c.contig,
                 g.c.position == gt.c.position,
                 g.c.reference == gt.c.reference,
@@ -112,7 +113,7 @@ def get(vcf_id, query, with_stats=True, truth_vcf_id=None):
         q = _add_ordering(q, g, 'Integer', 'position', 'asc')
 
         genotypes = [dict(g) for g in con.execute(q).fetchall()]
-    stats = calculate_stats(vcf_id, truth_vcf_id, query) if with_stats else {}
+    stats = calculate_stats(vcf_id, validate_vcf_id, query) if with_stats else {}
     return {'records': genotypes, 'stats': stats}
 
 

cycledash/runs.py

@@ -18,19 +18,29 @@ class CollisionError(Exception):
     pass
 
 
-def get_run(run_id):
-    """Return a run with a given ID, and the spec and list of contigs for that
+def get_vcf(vcf_id):
+    """Return a vcf with a given ID, and the spec and list of contigs for that
     run for use by the /examine page."""
     with tables(db, 'vcfs') as (con, vcfs):
-        q = select(vcfs.c).where(vcfs.c.id == run_id)
-        run = dict(con.execute(q).fetchone())
-    run['spec'] = genotypes.spec(run_id)
-    run['contigs'] = genotypes.contigs(run_id)
-    return run
+        q = select(vcfs.c).where(vcfs.c.id == vcf_id)
+        vcf = dict(con.execute(q).fetchone())
+    vcf['spec'] = genotypes.spec(vcf_id)
+    vcf['contigs'] = genotypes.contigs(vcf_id)
+    return vcf
 
 
-def create_run():
-    """Create a new run, inserting it into the vcfs table and starting workers.
+def get_related_vcfs(vcf):
+    """Return a list of vcfs in the same project as vcf."""
+    with tables(db, 'vcfs') as (con, vcfs):
+        q = select(vcfs.c).where(
+            vcfs.c.project_id == vcf['project_id']).where(
+                vcfs.c.id != vcf['id'])
+        vcfs = [dict(v) for v in con.execute(q).fetchall()]
+    return vcfs
+
+
+def create_vcf():
+    """Create a new vcf, inserting it into the vcfs table and starting workers.
 
     This raises an exception if anything goes wrong.
     """

cycledash/static/css/examine.css

@@ -293,6 +293,15 @@ table.vcf-table {
   }
 }
 
+/* VCFValidation */
+#vcf-validations {
+  margin: 11px;
+}
+#vcf-validations select {
+  width: 500px;
+  margin-left: 13px;
+}
+
 /* ExamineInformation */
 .examine-information {
   max-width: 600px;

cycledash/static/js/examine/RecordActions.js

@@ -5,6 +5,7 @@ var ACTION_TYPES = {
   DELETE_COMMENT: 'DELETE_COMMENT',
   REQUEST_PAGE: 'REQUEST_PAGE',
   SELECT_RECORD: 'SELECT_RECORD',
+  SELECT_VALIDATION_VCF: 'SELECT_VALIDATION_VCF',
   SET_COMMENT: 'SET_COMMENT',
   SET_QUERY: 'SET_QUERY',
   SET_VIEWER_OPEN: 'SET_VIEWER_OPEN',
@@ -36,6 +37,12 @@ function getRecordActions(dispatcher) {
         record
       });
     },
+    selectValidationVcf: function(validationVcfId) {
+      dispatcher.dispatch({
+        actionType: ACTION_TYPES.SELECT_VALIDATION_VCF,
+        validationVcfId
+      });
+    },
     setViewerOpen: function(isOpen) {
       dispatcher.dispatch({
         actionType: ACTION_TYPES.SET_VIEWER_OPEN,

cycledash/static/js/examine/RecordStore.js

@@ -41,6 +41,8 @@ function createRecordStore(run, igvHttpfsUrl, dispatcher, opt_testDataSource) {
       selectedRecord = null,
       isViewerOpen = false,
 
+      selectedVcfId = null,
+
       filters = [],
       sortBys = DEFAULT_SORT_BYS,
       range = ENTIRE_GENOME,
@@ -89,6 +91,10 @@ function createRecordStore(run, igvHttpfsUrl, dispatcher, opt_testDataSource) {
         selectedRecord = action.record;
         notifyChange();
         break;
+      case ACTION_TYPES.SELECT_VALIDATION_VCF:
+        selectedVcfId = parseInt(action.validationVcfId);
+        updateGenotypes({append: false});
+        break;
       case ACTION_TYPES.SET_VIEWER_OPEN:
         isViewerOpen = action.isOpen;
         notifyChange();
@@ -133,8 +139,8 @@ function createRecordStore(run, igvHttpfsUrl, dispatcher, opt_testDataSource) {
       page = 0;
     }
 
-    var query = queryFrom(range, filters, sortBys, page, limit);
-    setSearchStringToQuery(query);
+    var query = queryFrom(range, filters, sortBys, page, limit, selectedVcfId);
+    setQueryStringToQuery(query);
 
     // If we're not just appending records, reset the selected records (as the
     // table is now invalidated).
@@ -343,7 +349,7 @@ function createRecordStore(run, igvHttpfsUrl, dispatcher, opt_testDataSource) {
   }
 
   // Returns a JS object query for sending to the backend.
-  function queryFrom(range, filters, sortBy, page, limit) {
+  function queryFrom(range, filters, sortBy, page, limit, selectedVcfId) {
     if (sortBy[0].columnName == 'position') {
       sortBy = DEFAULT_SORT_BYS.map(sb => {
         sb.order = sortBys[0].order;
@@ -355,7 +361,8 @@ function createRecordStore(run, igvHttpfsUrl, dispatcher, opt_testDataSource) {
       filters,
       sortBy,
       page,
-      limit
+      limit,
+      selectedVcfId
     };
   }
 
@@ -369,7 +376,7 @@ function createRecordStore(run, igvHttpfsUrl, dispatcher, opt_testDataSource) {
     return decodeURIComponent(q.replace(/\+/g, '%20'));
   }
 
-  function setSearchStringToQuery(query) {
+  function setQueryStringToQuery(query) {
     var queryString = encodeURIPlus(QueryLanguage.toString(query));
     window.history.replaceState(null, null, '?query=' + queryString);
   }
@@ -439,7 +446,7 @@ function createRecordStore(run, igvHttpfsUrl, dispatcher, opt_testDataSource) {
 
   return {
     getState: function() {
-      var query = queryFrom(range, filters, sortBys, page, limit);
+      var query = queryFrom(range, filters, sortBys, page, limit, selectedVcfId);
       return {
         columns,
         contigs,
@@ -453,6 +460,7 @@ function createRecordStore(run, igvHttpfsUrl, dispatcher, opt_testDataSource) {
         range,
         records,
         selectedRecord,
+        selectedVcfId,
         sortBys,
         stats
       };

cycledash/static/js/examine/components/ExamineInformation.js

@@ -12,10 +12,8 @@ var ExamineInformation = React.createClass({
     return (
         <div className="examine-information">
           <dl>
-            <dt>Run ID</dt> <dd>{run.id}</dd>
             <dt>VCF URI</dt> <dd>{run.uri}</dd>
             <dt>Caller</dt> <dd>{run.caller_name}</dd>
-            <dt>Dataset</dt> <dd>{run.dataset_name}</dd>
             <dt>Submitted At</dt> <dd>{run.created_at}</dd>
           </dl>
         </div>

cycledash/static/js/examine/components/ExaminePage.js

@@ -6,16 +6,18 @@ var React = require('react'),
     VCFTable = require('./VCFTable'),
     QueryBox = require('./QueryBox'),
     Downloads = require('./Downloads'),
-    ExamineInformation = require('./ExamineInformation');
+    ExamineInformation = require('./ExamineInformation'),
+    VCFValidation = require('./VCFValidation');
 
 
 // The root component of the page.
 var ExaminePage = React.createClass({
   propTypes: {
     recordStore: React.PropTypes.object.isRequired,
     recordActions: React.PropTypes.object.isRequired,
-    run: React.PropTypes.object,
-    igvHttpfsUrl: React.PropTypes.string.isRequired
+    vcf: React.PropTypes.object,
+    igvHttpfsUrl: React.PropTypes.string.isRequired,
+    vcfs: React.PropTypes.arrayOf(React.PropTypes.object)
   },
   getInitialState: function() {
     return this.props.recordStore.getState();
@@ -47,6 +49,9 @@ var ExaminePage = React.createClass({
   handlePreviousRecord: function() {
     this.moveSelectionInDirection(-1);
   },
+  handleValidationVcfChange: function(selectedVcfId) {
+    this.props.recordActions.selectValidationVcf(selectedVcfId);
+  },
   moveSelectionInDirection: function(delta) {
     if (!this.state.selectedRecord) return;
     var records = this.state.records,
@@ -72,13 +77,18 @@ var ExaminePage = React.createClass({
       <div className="examine-page">
         <StatsSummary hasLoaded={state.hasLoaded}
                       stats={state.stats} />
-        <ExamineInformation run={props.run}/>
+        <ExamineInformation run={props.vcf}/>
+        {props.vcfs ?
+         <VCFValidation vcfs={props.vcfs}
+                        selectedVcfId={state.selectedVcfId}
+                        handleValidationVcfChange={this.handleValidationVcfChange} /> :
+          null}
         <QueryBox columns={state.columns}
                   hasPendingRequest={state.hasPendingRequest}
                   loadError={state.loadError}
                   query={state.query}
                   handleQueryChange={this.handleQueryChange} />
-        <Downloads query={state.query} run_id={props.run.id} />
+        <Downloads query={state.query} run_id={props.vcf.id} />
         <VCFTable ref="vcfTable"
                   hasLoaded={state.hasLoaded}
                   records={state.records}
@@ -94,9 +104,9 @@ var ExaminePage = React.createClass({
                   handleOpenViewer={this.handleOpenViewer}
                   handleSetComment={this.handleSetComment}
                   handleDeleteComment={this.handleDeleteComment} />
-        <BioDalliance vcfPath={props.run.uri}
-                      normalBamPath={props.run.normal_bam_uri}
-                      tumorBamPath={props.run.tumor_bam_uri}
+        <BioDalliance vcfPath={props.vcf.uri}
+                      normalBamPath={props.vcf.normal_bam_uri}
+                      tumorBamPath={props.vcf.tumor_bam_uri}
                       igvHttpfsUrl={props.igvHttpfsUrl}
                       selectedRecord={state.selectedRecord}
                       isOpen={state.isViewerOpen}
@@ -109,4 +119,3 @@ var ExaminePage = React.createClass({
 });
 
 module.exports = ExaminePage;
-

cycledash/static/js/examine/components/VCFValidation.js

@@ -0,0 +1,30 @@
+"use strict";
+
+var React = require('react');
+
+var VCFValidation = React.createClass({
+  propTypes: {
+    vcfs: React.PropTypes.arrayOf(React.PropTypes.object).isRequired,
+    selectedVcfId: React.PropTypes.number,
+    handleValidationVcfChange: React.PropTypes.func.isRequired
+  },
+  handleSelect: function(evt) {
+    this.props.handleValidationVcfChange(evt.target.value);
+  },
+  render: function() {
+    var vcfs = [{id: null, uri: '---'}].concat(
+      this.props.vcfs).map(
+        v => <option value={v.id} key={v.uri}>{v.uri}</option>);
+    return (
+      <div id='vcf-validations'>
+        Validate against:
+        <select onChange={this.handleSelect}
+                value={this.props.selectedVcfId}>
+          {vcfs}
+        </select>
+      </div>
+    );
+  }
+});
+
+module.exports = VCFValidation;

cycledash/static/js/examine/examine.js

@@ -7,12 +7,13 @@ var React = require('react'),
     getRecordActions = require('./RecordActions').getRecordActions;
 
 
-window.renderExaminePage = function(el, run, igvHttpfsUrl) {
+window.renderExaminePage = function(el, vcf, vcfs, igvHttpfsUrl) {
   var dispatcher = new Dispatcher();
   var recordActions = getRecordActions(dispatcher);
-  var recordStore = createRecordStore(run, igvHttpfsUrl, dispatcher);
+  var recordStore = createRecordStore(vcf, igvHttpfsUrl, dispatcher);
   React.render(<ExaminePage recordStore={recordStore}
                             recordActions={recordActions}
-                            run={run}
+                            vcfs={vcfs}
+                            vcf={vcf}
                             igvHttpfsUrl={igvHttpfsUrl} />, el);
 };

cycledash/static/js/runs/components/RunsPage.js

@@ -44,7 +44,8 @@ var RunsPage = React.createClass({
     var projectTables = _.chain(this.filteredProjects())
         .sortBy(project => {
           var vcf = project.vcfs[0];
-          // to sort by the descending ID, assumuning project.runs is already sorted by descending ID
+          // Sort by the descending ID, assuming project.runs is already sorted
+          // by descending ID.
           return vcf ?  -vcf.id : -100;
         }).map(function(project) {
             return <ProjectTable key={project.name}
@@ -62,7 +63,8 @@ var RunsPage = React.createClass({
         <h1>
           Data Directory
           {!this.state.displayProjectForm ?
-           <button className='btn btn-default' id='new-project' onClick={() => this.setDisplayProjectForm(true)}>
+           <button className='btn btn-default' id='new-project'
+                   onClick={() => this.setDisplayProjectForm(true)}>
              New Project
            </button> : null}
         </h1>

cycledash/templates/examine.html

@@ -17,7 +17,8 @@
 <script type="text/javascript" src="/static/js/dist/bundled.js"></script>
 <script>
  window.renderExaminePage(document.getElementById('examine'),
-                          {{ run | tojson }},
+                          {{ vcf | tojson }},
+                          {{ vcfs | tojson }},
                           {{ config['IGV_HTTPFS_URL'] | tojson }});
 </script>
 {% endblock%}

cycledash/views.py

@@ -40,12 +40,12 @@ def about():
 @app.route('/runs', methods=['POST', 'GET'])
 def list_runs():
     if request.method == 'POST':
-        return cycledash.runs.create_run()
+        return cycledash.runs.create_vcf()
     elif request.method == 'GET':
         return cycledash.projects.get_projects_tree()
 
 
-@app.route('/tasks/<run_id>', methods=['GET', 'DELETE'])
+@app.route('/tasks/<vcf_id>', methods=['GET', 'DELETE'])
 def get_tasks(run_id):
     if request.method == 'GET':
         tasks = cycledash.tasks.get_tasks(run_id)
@@ -108,7 +108,10 @@ def bam(bam_id):
 
 @app.route('/runs/<run_id>/examine')
 def examine(run_id):
-    return render_template('examine.html', run=cycledash.runs.get_run(run_id))
+    vcf = cycledash.runs.get_vcf(run_id)
+    return render_template('examine.html',
+                           vcf=vcf,
+                           vcfs=cycledash.runs.get_related_vcfs(vcf))
 
 
 @app.route('/runs/<run_id>/genotypes')