Merge branch 'release/0.10.1'

statgen · Jan 15, 2020 · e3c5f8b · e3c5f8b
2 parents ef66428 + c8f6b20
commit e3c5f8b
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Showing 22 changed files with 298 additions and 160 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -1,6 +1,7 @@
 language: node_js
 node_js:
   - "lts/carbon"
+  - "lts/erbium"
 cache:
   yarn: true
   directories:
@@ -15,7 +16,6 @@ branches:
     - develop
 notifications:
   email:
-    - [email protected]
     - [email protected]
   slack:
     secure: 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
diff --git a/assets/js/app/Dashboard.js b/assets/js/app/Dashboard.js
@@ -789,9 +789,11 @@ LocusZoom.Dashboard.Component.Button = function(parent) {
 LocusZoom.Dashboard.Components.add('title', function(layout) {
     LocusZoom.Dashboard.Component.apply(this, arguments);
     this.show = function() {
-        this.div_selector = this.parent.selector.append('div')
-            .attr('class', 'lz-dashboard-title lz-dashboard-' + this.layout.position);
-        this.title_selector = this.div_selector.append('h3');
+        if (!this.div_selector) {
+            this.div_selector = this.parent.selector.append('div')
+                .attr('class', 'lz-dashboard-title lz-dashboard-' + this.layout.position);
+            this.title_selector = this.div_selector.append('h3');
+        }
         return this.update();
     };
     this.update = function() {
@@ -847,6 +849,7 @@ LocusZoom.Dashboard.Components.add('region_scale', function(layout) {
  * @augments LocusZoom.Dashboard.Component
  * @param {string} [layout.button_html="Download Image"]
  * @param {string} [layout.button_title="Download image of the current plot as locuszoom.svg"]
+ * @param {string} [layout.filename="locuszoom.svg"] The default filename to use when saving the image
  */
 LocusZoom.Dashboard.Components.add('download', function(layout) {
     LocusZoom.Dashboard.Component.apply(this, arguments);

diff --git a/assets/js/app/Data.js b/assets/js/app/Data.js
@@ -1035,17 +1035,16 @@ LocusZoom.Data.GeneSource.prototype.normalizeResponse = function (data) { return
 LocusZoom.Data.GeneSource.prototype.extractFields = function (data, fields, outnames, trans) { return data; };
 
 /**
- * Data Source for Gene Constraint Data, as fetched from the ExAC server (or compatible)
+ * Data Source for Gene Constraint Data, as fetched from the gnomAD server (or compatible)
  *
- * FIXME: The ExAc server has been decommissioned. This source is kept here to avoid breaking existing layouts; we may
- *  be able to restore this feature in the future once the gnomAD API is further developed
+ * In the past, this source used ExAC, which has been completely decommissioned. Since the old source referenced a
+ *  server that no longer exists, this was redefined in 0.11.0 in a backwards-incompatible manner.
  *
  * @public
  * @class
  * @augments LocusZoom.Data.Source
 */
 LocusZoom.Data.GeneConstraintSource = LocusZoom.Data.Source.extend(function(init) {
-    console.warn('The gene constraint source depends on a server (ExAC) that is no longer active. This information may not be displayed.');
     this.parseInit(init);
 }, 'GeneConstraintLZ');
 
@@ -1060,46 +1059,53 @@ LocusZoom.Data.GeneConstraintSource.prototype.getCacheKey = function(state, chai
 };
 
 LocusZoom.Data.GeneConstraintSource.prototype.fetchRequest = function(state, chain, fields) {
-    var geneids = [];
-    chain.body.forEach(function(gene) {
-        var gene_id = gene.gene_id;
-        if (gene_id.indexOf('.')) {
-            gene_id = gene_id.substr(0, gene_id.indexOf('.'));
-        }
-        geneids.push(gene_id);
+    var build = state.genome_build || this.params.build;
+    if (!build) {
+        throw new Error(['Data source', this.constructor.SOURCE_NAME, 'requires that you specify a genome_build'].join(' '));
+    }
+
+    var query = chain.body.map(function (gene) {
+        var gene_name = gene.gene_name;
+        // GraphQL alias names must match a specific set of allowed characters: https://stackoverflow.com/a/45757065/1422268
+        var alias = gene.gene_name.replace(/[^A-Za-z0-9_]/g, '_');
+        // Each gene is a separate graphQL query, grouped into one request using aliases
+        return alias + ': gene(gene_symbol: "' + gene_name + '", reference_genome: ' + build + ') { gnomad_constraint { exp_syn obs_syn syn_z oe_syn oe_syn_lower oe_syn_upper exp_mis obs_mis mis_z oe_mis oe_mis_lower oe_mis_upper exp_lof obs_lof pLI oe_lof oe_lof_lower oe_lof_upper } } ';
     });
+
+    if (!query.length) {
+        // If there are no genes, skip the network request
+        return Promise.resolve({ data: null });
+    }
+
+    query = '{' + query.join(' ') + ' }'; // GraphQL isn't quite JSON; items are separated by spaces but not commas
     var url = this.getURL(state, chain, fields);
-    var body = 'geneids=' + encodeURIComponent(JSON.stringify(geneids));
-    var headers = {
-        'Content-Type': 'application/x-www-form-urlencoded'
-    };
+    // See: https://graphql.org/learn/serving-over-http/
+    var body = JSON.stringify({ query: query });
+    var headers = { 'Content-Type': 'application/json' };
     return LocusZoom.createCORSPromise('POST', url, body, headers);
 };
 
 LocusZoom.Data.GeneConstraintSource.prototype.combineChainBody = function (data, chain, fields, outnames, trans) {
     if (!data) {
         return chain;
     }
-    var constraint_fields = ['bp', 'exp_lof', 'exp_mis', 'exp_syn', 'lof_z', 'mis_z', 'mu_lof', 'mu_mis','mu_syn', 'n_exons', 'n_lof', 'n_mis', 'n_syn', 'pLI', 'syn_z'];
-    chain.body.forEach(function(gene, i) {
-        var gene_id = gene.gene_id;
-        if (gene_id.indexOf('.')) {
-            gene_id = gene_id.substr(0, gene_id.indexOf('.'));
-        }
-        constraint_fields.forEach(function(field) {
-            // Do not overwrite any fields defined in the original gene source
-            if (typeof chain.body[i][field] != 'undefined') { return; }
-            if (data[gene_id]) {
-                var val = data[gene_id][field];
-                if (typeof val == 'number' && val.toString().indexOf('.') !== -1) {
-                    val = parseFloat(val.toFixed(2));
+
+    chain.body.forEach(function(gene) {
+        // Find payload keys that match gene names in this response
+        var alias = gene.gene_name.replace(/[^A-Za-z0-9_]/g, '_');  // aliases are modified gene names
+        var constraint = data[alias] && data[alias]['gnomad_constraint']; // gnomad API has two ways of specifying missing data for a requested gene
+        if (constraint) {
+            // Add all fields from constraint data- do not override fields present in the gene source
+            Object.keys(constraint).forEach(function (key) {
+                var val = constraint[key];
+                if (typeof gene[key] === 'undefined') {
+                    if (typeof val == 'number' && val.toString().indexOf('.') !== -1) {
+                        val = parseFloat(val.toFixed(2));
+                    }
+                    gene[key] = val;   // These two sources are both designed to bypass namespacing
                 }
-                chain.body[i][field] = val;
-            } else {
-                // If the gene did not come back in the response then set the same field with a null values
-                chain.body[i][field] = null;
-            }
-        });
+            });
+        }
     });
     return chain.body;
 };

diff --git a/assets/js/app/Layouts.js b/assets/js/app/Layouts.js
@@ -231,6 +231,12 @@ LocusZoom.Layouts.add('tooltip', 'standard_genes', {
     html: '<h4><strong><i>{{gene_name|htmlescape}}</i></strong></h4>'
         + 'Gene ID: <a href="https://useast.ensembl.org/homo_sapiens/Gene/Summary?g={{gene_id|htmlescape}}&db=core" target="_blank" rel="noopener">{{gene_id|htmlescape}}</a><br>'
         + 'Transcript ID: <strong>{{transcript_id|htmlescape}}</strong><br>'
+        + '{{#if pLI}}<table>'
+        + '<tr><th>Constraint</th><th>Expected variants</th><th>Observed variants</th><th>Const. Metric</th></tr>'
+        + '<tr><td>Synonymous</td><td>{{exp_syn}}</td><td>{{obs_syn}}</td><td>z = {{syn_z}}<br>o/e = {{oe_syn}} ({{oe_syn_lower}} - {{oe_syn_upper}})</td></tr>'
+        + '<tr><td>Missense</td><td>{{exp_mis}}</td><td>{{obs_mis}}</td><td>z = {{mis_z}}<br>o/e = {{oe_mis}} ({{oe_mis_lower}} - {{oe_mis_upper}})</td></tr>'
+        + '<tr><td>pLoF</td><td>{{exp_lof}}</td><td>{{obs_lof}}</td><td>pLI = {{pLI}}<br>o/e = {{oe_lof}} ({{oe_lof_lower}} - {{oe_lof_upper}})</td></tr>'
+        + '</table><br>{{/if}}'
         + '<a href="https://gnomad.broadinstitute.org/gene/{{gene_id|htmlescape}}" target="_blank" rel="noopener">More data on gnomAD</a>'
 });
 
@@ -463,10 +469,10 @@ LocusZoom.Layouts.add('data_layer', 'phewas_pvalues', {
 });
 
 LocusZoom.Layouts.add('data_layer', 'genes', {
-    namespace: { 'gene': 'gene' },
+    namespace: { 'gene': 'gene', 'constraint': 'constraint' },
     id: 'genes',
     type: 'genes',
-    fields: ['{{namespace[gene]}}all'],
+    fields: ['{{namespace[gene]}}all', '{{namespace[constraint]}}all'],
     id_field: 'gene_id',
     behaviors: {
         onmouseover: [

diff --git a/assets/js/app/LocusZoom.js b/assets/js/app/LocusZoom.js
@@ -2,7 +2,7 @@
  * @namespace
  */
 var LocusZoom = {
-    version: '0.10.0'
+    version: '0.10.1'
 };
 
 /**

diff --git a/dist/locuszoom.app.js b/dist/locuszoom.app.js
@@ -39,7 +39,7 @@
         }    // ESTemplate: module content goes here
         // ESTemplate: module content goes here
         ;
-        var LocusZoom = { version: '0.10.0' };
+        var LocusZoom = { version: '0.10.1' };
         /**
  * Populate a single element with a LocusZoom plot.
  * selector can be a string for a DOM Query or a d3 selector.
@@ -1024,7 +1024,7 @@
                     'unselected'
                 ]
             },
-            html: '<h4><strong><i>{{gene_name|htmlescape}}</i></strong></h4>' + 'Gene ID: <a href="https://useast.ensembl.org/homo_sapiens/Gene/Summary?g={{gene_id|htmlescape}}&db=core" target="_blank" rel="noopener">{{gene_id|htmlescape}}</a><br>' + 'Transcript ID: <strong>{{transcript_id|htmlescape}}</strong><br>' + '<a href="https://gnomad.broadinstitute.org/gene/{{gene_id|htmlescape}}" target="_blank" rel="noopener">More data on gnomAD</a>'
+            html: '<h4><strong><i>{{gene_name|htmlescape}}</i></strong></h4>' + 'Gene ID: <a href="https://useast.ensembl.org/homo_sapiens/Gene/Summary?g={{gene_id|htmlescape}}&db=core" target="_blank" rel="noopener">{{gene_id|htmlescape}}</a><br>' + 'Transcript ID: <strong>{{transcript_id|htmlescape}}</strong><br>' + '{{#if pLI}}<table>' + '<tr><th>Constraint</th><th>Expected variants</th><th>Observed variants</th><th>Const. Metric</th></tr>' + '<tr><td>Synonymous</td><td>{{exp_syn}}</td><td>{{obs_syn}}</td><td>z = {{syn_z}}<br>o/e = {{oe_syn}} ({{oe_syn_lower}} - {{oe_syn_upper}})</td></tr>' + '<tr><td>Missense</td><td>{{exp_mis}}</td><td>{{obs_mis}}</td><td>z = {{mis_z}}<br>o/e = {{oe_mis}} ({{oe_mis_lower}} - {{oe_mis_upper}})</td></tr>' + '<tr><td>pLoF</td><td>{{exp_lof}}</td><td>{{obs_lof}}</td><td>pLI = {{pLI}}<br>o/e = {{oe_lof}} ({{oe_lof_lower}} - {{oe_lof_upper}})</td></tr>' + '</table><br>{{/if}}' + '<a href="https://gnomad.broadinstitute.org/gene/{{gene_id|htmlescape}}" target="_blank" rel="noopener">More data on gnomAD</a>'
         });
         LocusZoom.Layouts.add('tooltip', 'standard_intervals', {
             namespace: { 'intervals': 'intervals' },
@@ -1357,10 +1357,16 @@
             }
         });
         LocusZoom.Layouts.add('data_layer', 'genes', {
-            namespace: { 'gene': 'gene' },
+            namespace: {
+                'gene': 'gene',
+                'constraint': 'constraint'
+            },
             id: 'genes',
             type: 'genes',
-            fields: ['{{namespace[gene]}}all'],
+            fields: [
+                '{{namespace[gene]}}all',
+                '{{namespace[constraint]}}all'
+            ],
             id_field: 'gene_id',
             behaviors: {
                 onmouseover: [{
@@ -7348,8 +7354,10 @@
         LocusZoom.Dashboard.Components.add('title', function (layout) {
             LocusZoom.Dashboard.Component.apply(this, arguments);
             this.show = function () {
-                this.div_selector = this.parent.selector.append('div').attr('class', 'lz-dashboard-title lz-dashboard-' + this.layout.position);
-                this.title_selector = this.div_selector.append('h3');
+                if (!this.div_selector) {
+                    this.div_selector = this.parent.selector.append('div').attr('class', 'lz-dashboard-title lz-dashboard-' + this.layout.position);
+                    this.title_selector = this.div_selector.append('h3');
+                }
                 return this.update();
             };
             this.update = function () {
@@ -7411,6 +7419,7 @@
  * @augments LocusZoom.Dashboard.Component
  * @param {string} [layout.button_html="Download Image"]
  * @param {string} [layout.button_title="Download image of the current plot as locuszoom.svg"]
+ * @param {string} [layout.filename="locuszoom.svg"] The default filename to use when saving the image
  */
         LocusZoom.Dashboard.Components.add('download', function (layout) {
             LocusZoom.Dashboard.Component.apply(this, arguments);
@@ -9337,17 +9346,16 @@
             return data;
         };
         /**
- * Data Source for Gene Constraint Data, as fetched from the ExAC server (or compatible)
+ * Data Source for Gene Constraint Data, as fetched from the gnomAD server (or compatible)
  *
- * FIXME: The ExAc server has been decommissioned. This source is kept here to avoid breaking existing layouts; we may
- *  be able to restore this feature in the future once the gnomAD API is further developed
+ * In the past, this source used ExAC, which has been completely decommissioned. Since the old source referenced a
+ *  server that no longer exists, this was redefined in 0.11.0 in a backwards-incompatible manner.
  *
  * @public
  * @class
  * @augments LocusZoom.Data.Source
 */
         LocusZoom.Data.GeneConstraintSource = LocusZoom.Data.Source.extend(function (init) {
-            console.warn('The gene constraint source depends on a server (ExAC) that is no longer active. This information may not be displayed.');
             this.parseInit(init);
         }, 'GeneConstraintLZ');
         LocusZoom.Data.GeneConstraintSource.prototype.getURL = function () {
@@ -9360,61 +9368,55 @@
             return this.url + JSON.stringify(state);
         };
         LocusZoom.Data.GeneConstraintSource.prototype.fetchRequest = function (state, chain, fields) {
-            var geneids = [];
-            chain.body.forEach(function (gene) {
-                var gene_id = gene.gene_id;
-                if (gene_id.indexOf('.')) {
-                    gene_id = gene_id.substr(0, gene_id.indexOf('.'));
-                }
-                geneids.push(gene_id);
+            var build = state.genome_build || this.params.build;
+            if (!build) {
+                throw new Error([
+                    'Data source',
+                    this.constructor.SOURCE_NAME,
+                    'requires that you specify a genome_build'
+                ].join(' '));
+            }
+            var query = chain.body.map(function (gene) {
+                var gene_name = gene.gene_name;
+                // GraphQL alias names must match a specific set of allowed characters: https://stackoverflow.com/a/45757065/1422268
+                var alias = gene.gene_name.replace(/[^A-Za-z0-9_]/g, '_');
+                // Each gene is a separate graphQL query, grouped into one request using aliases
+                return alias + ': gene(gene_symbol: "' + gene_name + '", reference_genome: ' + build + ') { gnomad_constraint { exp_syn obs_syn syn_z oe_syn oe_syn_lower oe_syn_upper exp_mis obs_mis mis_z oe_mis oe_mis_lower oe_mis_upper exp_lof obs_lof pLI oe_lof oe_lof_lower oe_lof_upper } } ';
             });
+            if (!query.length) {
+                // If there are no genes, skip the network request
+                return Promise.resolve({ data: null });
+            }
+            query = '{' + query.join(' ') + ' }';
+            // GraphQL isn't quite JSON; items are separated by spaces but not commas
             var url = this.getURL(state, chain, fields);
-            var body = 'geneids=' + encodeURIComponent(JSON.stringify(geneids));
-            var headers = { 'Content-Type': 'application/x-www-form-urlencoded' };
+            // See: https://graphql.org/learn/serving-over-http/
+            var body = JSON.stringify({ query: query });
+            var headers = { 'Content-Type': 'application/json' };
             return LocusZoom.createCORSPromise('POST', url, body, headers);
         };
         LocusZoom.Data.GeneConstraintSource.prototype.combineChainBody = function (data, chain, fields, outnames, trans) {
             if (!data) {
                 return chain;
             }
-            var constraint_fields = [
-                'bp',
-                'exp_lof',
-                'exp_mis',
-                'exp_syn',
-                'lof_z',
-                'mis_z',
-                'mu_lof',
-                'mu_mis',
-                'mu_syn',
-                'n_exons',
-                'n_lof',
-                'n_mis',
-                'n_syn',
-                'pLI',
-                'syn_z'
-            ];
-            chain.body.forEach(function (gene, i) {
-                var gene_id = gene.gene_id;
-                if (gene_id.indexOf('.')) {
-                    gene_id = gene_id.substr(0, gene_id.indexOf('.'));
-                }
-                constraint_fields.forEach(function (field) {
-                    // Do not overwrite any fields defined in the original gene source
-                    if (typeof chain.body[i][field] != 'undefined') {
-                        return;
-                    }
-                    if (data[gene_id]) {
-                        var val = data[gene_id][field];
-                        if (typeof val == 'number' && val.toString().indexOf('.') !== -1) {
-                            val = parseFloat(val.toFixed(2));
+            chain.body.forEach(function (gene) {
+                // Find payload keys that match gene names in this response
+                var alias = gene.gene_name.replace(/[^A-Za-z0-9_]/g, '_');
+                // aliases are modified gene names
+                var constraint = data[alias] && data[alias]['gnomad_constraint'];
+                // gnomad API has two ways of specifying missing data for a requested gene
+                if (constraint) {
+                    // Add all fields from constraint data- do not override fields present in the gene source
+                    Object.keys(constraint).forEach(function (key) {
+                        var val = constraint[key];
+                        if (typeof gene[key] === 'undefined') {
+                            if (typeof val == 'number' && val.toString().indexOf('.') !== -1) {
+                                val = parseFloat(val.toFixed(2));
+                            }
+                            gene[key] = val;    // These two sources are both designed to bypass namespacing
                         }
-                        chain.body[i][field] = val;
-                    } else {
-                        // If the gene did not come back in the response then set the same field with a null values
-                        chain.body[i][field] = null;
-                    }
-                });
+                    });
+                }
             });
             return chain.body;
         };

diff --git a/dist/locuszoom.app.js.map b/dist/locuszoom.app.js.map
diff --git a/dist/locuszoom.app.min.js b/dist/locuszoom.app.min.js
diff --git a/dist/locuszoom.app.min.js.map b/dist/locuszoom.app.min.js.map