Merge branch 'release/0.1.9'

assets/js/pages/gwas_region.js

@@ -2,9 +2,9 @@ import Vue from 'vue';
 import App from '../../vue/gwas_region.vue';
 
 import { paramsFromUrl } from 'locuszoom/dist/ext/lz-dynamic-urls.min';
-import { stateUrlMapping } from 'locuszoom-tabix/src/util/lz-helpers';
 
-import { getBasicSources, createStudyLayout, getBasicLayout } from 'locuszoom-tabix/src/util/lz-helpers';
+import { stateUrlMapping, getBasicSources, createStudyLayout, getBasicLayout } from 'localzoom/src/util/lz-helpers';
+import count_region_view from 'localzoom/src/util/metrics';
 import { createStudyAssocSources } from '../util/lz-helpers';
 
 function makePlot(template_vars) {
@@ -38,4 +38,6 @@ function makePlot(template_vars) {
     })}).$mount('#app');
 }
 
+// On page load, generate a plot, and send Google Analytics metrics for first plot rendered
 window.lz_widget = makePlot(window.template_args);
+count_region_view();

assets/js/pages/gwas_summary.js

@@ -44,6 +44,7 @@ function createTopHitsTable(selector, data, region_url) {
             {
                 title: 'Nearest gene(s)',
                 field: 'nearest_genes',
+                sorter: 'string',
                 formatter: cell => {
                     const genes = cell.getValue() || [];  // There will be studies that predate this feature, and won't have a value
                     // Convert the list of ensg/symbol objects to a string- eventually we can add links to ext DB

assets/js/pages/gwas_upload.js

@@ -9,8 +9,8 @@ import pako from 'pako';
 
 import App from '../../vue/gwas_upload.vue';
 
-import { isHeader } from 'locuszoom-tabix/src/gwas/sniffers';
-import { makeParser } from 'locuszoom-tabix/src/gwas/parsers';
+import { isHeader } from 'localzoom/src/gwas/sniffers';
+import { makeParser } from 'localzoom/src/gwas/parsers';
 
 const PREVIEW_BYTES = 5000;  // enough for 50-100 lines
 const MAX_UPLOAD_SIZE = 1048576 * 1000; // 1000 MiB # FIXME: Currently upload limit is only implemented in the frontend
@@ -185,7 +185,7 @@ fileField.addEventListener('click', function(e) {
     e.target.value = null;
 });
 
-fileField.addEventListener('change', function (e) {
+fileField.addEventListener('change', function (event) {
     // Custom validators for uploaded file
     //  Ref: https://developer.mozilla.org/en-US/docs/Web/Guide/HTML/HTML5/Constraint_validation#Limiting_the_size_of_a_file_before_its_upload
     fileField.setCustomValidity('');

assets/js/util/lz-helpers.js

@@ -4,7 +4,7 @@
 
 import LocusZoom from 'locuszoom';
 
-import { sourceName} from 'locuszoom-tabix/src/util/lz-helpers';
+import { sourceName} from 'localzoom/src/util/lz-helpers';
 
 LocusZoom.KnownDataSources.extend('AssociationLZ', 'AssociationApi', {
     getURL(state, chain,fields) {

assets/js/util/pheweb_plots.js

@@ -20,6 +20,10 @@ function fmt(format) {
 
 function create_gwas_plot(variant_bins, unbinned_variants, {url_prefix = null, tooltip_template = null} = {}) {
     // FIXME: Replace global variables with options object
+    // Order from weakest to strongest pvalue, so that the strongest variant will be on top (z-order) and easily hoverable
+    // In the DOM, later siblings are displayed over top of (and occluding) earlier siblings.
+    unbinned_variants = _.sortBy(unbinned_variants, function(d) { return d.neg_log_pvalue; });
+
     const get_chrom_offsets = _.memoize(function() {
         const  chrom_padding = 2e7;
         const chrom_extents = {};
@@ -120,7 +124,7 @@ function create_gwas_plot(variant_bins, unbinned_variants, {url_prefix = null, t
         const plot_margin = {
             'left': 70,
             'right': 30,
-            'top': 10,
+            'top': 20,
             'bottom': 50,
         };
         const plot_width = svg_width - plot_margin.left - plot_margin.right;

assets/vue/gwas_region.vue

@@ -1,9 +1,9 @@
 <script>
     // Custom interactivity attached to the "GWAS Region/LocusZoom plot" page
-    import BatchSpec from 'locuszoom-tabix/src/components/BatchSpec.vue';
-    import BatchScroller from 'locuszoom-tabix/src/components/BatchScroller.vue';
-    import PlotPanes from 'locuszoom-tabix/src/components/PlotPanes.vue';
-    import RegionPicker from 'locuszoom-tabix/src/components/RegionPicker.vue';
+    import BatchSpec from 'localzoom/src/components/BatchSpec.vue';
+    import BatchScroller from 'localzoom/src/components/BatchScroller.vue';
+    import PlotPanes from 'localzoom/src/components/PlotPanes.vue';
+    import RegionPicker from 'localzoom/src/components/RegionPicker.vue';
 
     const MAX_REGION_SIZE = 1000000;
 

assets/vue/gwas_upload.vue

@@ -1,7 +1,7 @@
 <script>
     // Custom interactivity associated with the "Upload your own GWAS" page.
     // This enhances just one part of the upload form.
-    import AdderWizard from 'locuszoom-tabix/src/components/AdderWizard.vue';
+    import AdderWizard from 'localzoom/src/components/AdderWizard.vue';
 
     export default {
         name: 'gwas_upload',

locuszoom_plotting_service/gwas/migrations/0006_auto_20200214_1919.py

@@ -0,0 +1,17 @@
+# Generated by Django 2.0.13 on 2020-02-14 19:19
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('gwas', '0005_auto_20190929_0344'),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name='analysisinfo',
+            options={'verbose_name_plural': 'GWAS Analysis Metadata'},
+        ),
+    ]

locuszoom_plotting_service/templates/gwas/gwas_region.html

@@ -3,7 +3,7 @@
 
 {% block title %}Region plot- {{ gwas.label }}{% endblock %}
 {% block css %}
-  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/locuszoom@0.9.0/dist/locuszoom.css" type="text/css"/>
+  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/locuszoom@0.10.1/dist/locuszoom.css" type="text/css"/>
 {% endblock %}
 
 {% block content %}
@@ -41,31 +41,4 @@
   {#  {{ js_vars | json_script: 'js-vars' }}#}
   {#  Define the LocusZoom plot #}
   {% render_bundle 'gwas_region' %}
-
-  {% if GOOGLE_ANALYTICS_ID %}
-    <script>
-      // Track an aggregate sum of all possible region plots generated.
-      // This section contains a hack around the fact that there is no direct event for `history.pushState`
-      // Ref: https://stackoverflow.com/a/25673911/1422268
-      var _wr = function(type) {
-        var orig = history[type];
-        return function() {
-            var rv = orig.apply(this, arguments);
-            var e = new Event(type);
-            e.arguments = arguments;
-            window.dispatchEvent(e);
-            return rv;
-        };
-      };
-      // Monkey-patching: icky, but necessary.
-      history.pushState = _wr('pushState'); // Define a synthetic DOM event by wrapping the history function.
-
-      var listener = function() { gtag('event', 'regionview'); };
-      // Count a new region plot on page load, and whenever url changes (forward = pushState, back = popstate);
-      listener();
-      window.addEventListener('popstate', listener);
-      window.addEventListener('pushState', listener);  // synthetic event
-    </script>
-  {% endif %}
-
 {% endblock %}

package.json

@@ -31,8 +31,8 @@
     "d3": "3.5.16",
     "d3-tip": "0.9.0",
     "gwas-credible-sets": "^0.1.0",
-    "locuszoom": "0.10.0",
-    "locuszoom-tabix": "https://github.com/statgen/localzoom#918fd75",
+    "localzoom": "https://github.com/statgen/localzoom#v0.5.3",
+    "locuszoom": "https://github.com/statgen/locuszoom#42f7c64127893f5f1b00ddf9b81acf369179dc36",
     "pako": "^1.0.8",
     "underscore": "1.8.3",
     "vue": "^2.6.10",

requirements/base.txt

@@ -35,5 +35,5 @@ pyyaml  # Required for OpenAPI rendering
 boltons~=19.1
 scipy~=1.2
 python-magic==0.4.15
-zorp==0.1.1
+git+git://github.com/abought/zorp.git@893d383
 genelocator==1.1.1