Merge branch 'release/0.1.5'

.nvmrc

@@ -1 +1 @@
-lts/carbon
+lts/erbium

assets/js/pages/gwas_region.js

@@ -24,7 +24,8 @@ function makePlot(template_vars) {
         {
             lz_sources: getBasicSources(assoc_sources),
             lz_layout: getBasicLayout(state, panels, { responsive_resize: false }),
-            study_names: [template_vars.label]
+            study_names: [template_vars.label],
+            top_hits_url: template_vars.top_hits_url,
         }, template_vars,
         {
             genome_build: template_vars.build,

assets/js/pages/gwas_summary.js

@@ -13,7 +13,6 @@ function createTopHitsTable(selector, data, region_url) {
     data = data.filter(v => !!v.peak)
         .map(item => {
             // FIXME: Synthetic field; feed a marker into pheweb loader code for better tables in the future
-            // TODO: Get pheweb "nearest gene" annotations working (and make build agnostic)
             item.marker = `${item.chrom}: ${item.pos.toLocaleString()}`;
             return item;
         });

assets/vue/gwas_region.vue

@@ -1,30 +1,43 @@
 <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';
 
+    const MAX_REGION_SIZE = 1000000;
+
     export default {
         name: 'gwas_region',
         props: [
             'build', 'chr', 'start', 'end',
             'lz_layout',
             'lz_sources',
             'study_names',
+            'top_hits_url'
         ],
         data() {
             return {
+                // make constant available
+                max_region_size: MAX_REGION_SIZE,
                 message: '',
                 message_class: '',
 
                 // Allow initial state to be passed in, but then mutated as user navigates
                 c_chr: this.chr,
                 c_start: this.start,
-                c_end: this.end
-
+                c_end: this.end,
 
+                // Controls for "batch view" mode
+                batch_mode_active: false,
+                batch_mode_regions: [],
             };
         },
         methods: {
+            activateBatchMode(regions) {
+                this.batch_mode_active = true;
+                this.batch_mode_regions = regions;
+            },
             showMessage(message, style = 'text-danger') {
                 this.message = message;
                 this.message_class = style;
@@ -35,23 +48,59 @@
                 this.c_start = region.start;
                 this.c_end = region.end;
             },
+            fetchTopHits() {
+                // Used for batch mode "get top hits" button
+                // Fetch pre-computed top loci, in sorted order, and return list of [ {chr, start, end} ] entries
+                return fetch(this.top_hits_url)
+                    .then(resp => {
+                        if (resp.ok) {
+                            return resp.json();
+                        }
+                        throw new Error('Could not retrieve results');
+                    }).then(json => {
+                        // Convert the list of peaks (top hits) into manageable nearby regions (target +/- 250k)
+                        return json.unbinned_variants.filter(variant => !!variant.peak)
+                            .sort((a, b) => b.neg_log_pvalue - a.neg_log_pvalue)
+                            .map(variant => ({
+                                chr: variant.chrom,
+                                start: +variant.pos - 250000,
+                                end: +variant.pos + 250000
+                            }));
+                    });
+            }
         },
-        components: { PlotPanes, RegionPicker }
+        components: { BatchSpec, BatchScroller, PlotPanes, RegionPicker }
     }
 </script>
 
 <template>
   <div>
-    <div class="row">
-      <div class="col-md-8"></div>
-      <div class="col-md-4">
-        <region-picker
-            @ready="updateRegion"
-            @fail="showMessage"
-            class="float-right"
-            :build="build"
-            :max_range="500000"
-            search_url="https://portaldev.sph.umich.edu/api/v1/annotation/omnisearch/"/>
+    <div class="row" v-if="!batch_mode_active">
+      <div class="col-md-4"></div>
+      <div class="col-md-8">
+        <div class="d-flex justify-content-end">
+          <region-picker
+              @ready="updateRegion"
+              @fail="showMessage"
+              class="float-right"
+              :build="build"
+              :max_range="max_region_size"
+              search_url="https://portaldev.sph.umich.edu/api/v1/annotation/omnisearch/"/>
+          <batch-spec class="ml-1"
+                      :max_range="max_region_size"
+                      @ready="activateBatchMode">
+            <template #preset-button="{updateRegions}">
+              <button class="btn btn-warning" @click="updateRegions(fetchTopHits())">Get top hits</button>
+            </template>
+          </batch-spec>
+        </div>
+      </div>
+    </div>
+    <div class="row" v-else>
+      <div class="col-md-12">
+        <batch-scroller :regions="batch_mode_regions"
+                        @navigate="updateRegion"
+                        @cancel="batch_mode_active = false"/>
       </div>
     </div>
     <div class="row" v-if="message">
@@ -64,10 +113,8 @@
                     :assoc_layout="lz_layout" :assoc_sources="lz_sources"
                     :study_names="study_names" :has_credible_sets="true"
                     :build="build"
-                    :chr="c_chr" :start="c_start" :end="c_end" />
+                    :chr="c_chr" :start="c_start" :end="c_end"/>
       </div>
     </div>
   </div>
 </template>
-
-<style scoped></style>

locuszoom_plotting_service/gwas/views.py

@@ -214,6 +214,10 @@ def get_context_data(self, **kwargs):
                 reverse('apiv1:gwas-region', kwargs={'slug': gwas.slug}),
                 token
             ),
+            'top_hits_url': add_token(
+                reverse('gwas:manhattan-json', kwargs={'slug': gwas.slug}),
+                token,
+            ),
             'label': gwas.label,
             'build': gwas.build,
             # Default region for bare URLs is the top hit in the study

locuszoom_plotting_service/taskapp/tasks.py

@@ -8,6 +8,7 @@
 from django.db.models import signals
 from django.db import transaction
 from django.dispatch import receiver
+from django.urls import reverse
 from django.utils import timezone
 
 from zorp import (
@@ -156,8 +157,9 @@ def mark_success(self, fileset_id):
     metadata.save()
 
     # TODO: Render this as a nicer-looking template
+    log_url = reverse('gwas:gwas-ingest-log', kwargs={'slug': metadata.slug})
     send_mail('[locuszoom] Upload succeeded',
-              f'Your upload is done processing. Please visit https://{settings.LZ_OFFICIAL_DOMAIN}{metadata.get_absolute_url()} to see the Manhattan plot and begin exploring regions of your data.',  # noqa
+              f'Your upload is done processing. Please visit https://{settings.LZ_OFFICIAL_DOMAIN}{metadata.get_absolute_url()} to see the Manhattan plot and begin exploring regions of your data.\nBe sure to review the ingest logs for any warnings: https://{settings.LZ_OFFICIAL_DOMAIN}{log_url}',  # noqa
               '[email protected]',
               [metadata.owner.email])
 
@@ -176,8 +178,9 @@ def mark_failure(self, fileset_id):
     instance.save()
 
     metadata = instance.metadata
+    log_url = reverse('gwas:gwas-ingest-log', kwargs={'slug': metadata.slug})
     send_mail('[locuszoom] Upload failed',
-              f'Your upload failed to process. Please visit https://{settings.LZ_OFFICIAL_DOMAIN}{metadata.get_absolute_url()} to see the error logs.',  # noqa
+              f'Your upload failed to process. Please review the ingest logs for warnings and error messages: https://{settings.LZ_OFFICIAL_DOMAIN}{log_url}\nOr visit the upload page to change settings: https://{settings.LZ_OFFICIAL_DOMAIN}{metadata.get_absolute_url()}',  # noqa
               '[email protected]',
               [metadata.owner.email])
 

locuszoom_plotting_service/templates/base.html

@@ -39,8 +39,8 @@
 
   <link rel="icon" href="{% static 'images/favicons/favicon.ico' %}">
 
-  <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.1/css/bootstrap.min.css"
-        integrity="sha384-WskhaSGFgHYWDcbwN70/dfYBj47jz9qbsMId/iRN3ewGhXQFZCSftd1LZCfmhktB" crossorigin="anonymous">
+  <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/css/bootstrap.min.css"
+        integrity="sha384-Vkoo8x4CGsO3+Hhxv8T/Q5PaXtkKtu6ug5TOeNV6gBiFeWPGFN9MuhOf23Q9Ifjh" crossorigin="anonymous">
   <link href="{% static 'css/site.css' %}" rel="stylesheet">
   {% block css %}{% endblock %}
 </head>
@@ -131,15 +131,12 @@
 </footer>
 
 {# Javascript: global template code, plus custom items per page #}
-<script src="https://code.jquery.com/jquery-3.3.1.slim.min.js"
-        integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo"
-        crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.3/umd/popper.min.js"
-        integrity="sha384-ZMP7rVo3mIykV+2+9J3UJ46jBk0WLaUAdn689aCwoqbBJiSnjAK/l8WvCWPIPm49"
-        crossorigin="anonymous"></script>
-<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.1/js/bootstrap.min.js"
-        integrity="sha384-smHYKdLADwkXOn1EmN1qk/HfnUcbVRZyYmZ4qpPea6sjB/pTJ0euyQp0Mk8ck+5T"
-        crossorigin="anonymous"></script>
+<script src="https://code.jquery.com/jquery-3.4.1.slim.min.js" crossorigin="anonymous"
+        integrity="sha384-J6qa4849blE2+poT4WnyKhv5vZF5SrPo0iEjwBvKU7imGFAV0wwj1yYfoRSJoZ+n"></script>
+<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/umd/popper.min.js" crossorigin="anonymous"
+        integrity="sha384-Q6E9RHvbIyZFJoft+2mJbHaEWldlvI9IOYy5n3zV9zzTtmI3UksdQRVvoxMfooAo"></script>
+<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/js/bootstrap.min.js" crossorigin="anonymous"
+        integrity="sha384-wfSDF2E50Y2D1uUdj0O3uMBJnjuUD4Ih7YwaYd1iqfktj0Uod8GCExl3Og8ifwB6"></script>
 {% block javascript %}{% endblock javascript %}
 </body>
 </html>

locuszoom_plotting_service/templates/gwas/gwas_region.html

@@ -22,6 +22,9 @@
         <span class="text-muted">Uploaded by: {{ gwas.owner.display_name }}, {{ gwas.created | date }}</span>
         {% if gwas.is_public %}<span class="badge badge-info">Public</span> {% else %}<span class="badge badge-warning">Private</span>{% endif %}
         {% if gwas.pmid %}<a href="https://www.ncbi.nlm.nih.gov/pubmed/{{gwas.pmid}}" target="_blank" class="badge badge-dark">PubMed</a>{% endif %}
+        {% if gwas.owner == request.user %}(<a href="{% url 'gwas:edit' gwas.slug %}">edit</a>)
+          {% if not gwas.is_public %}(<a href="{% url 'gwas:share' gwas.slug %}">share</a>){% endif %}
+        {% endif %}
       </div>
     </div>
 

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-beta.2",
-    "locuszoom-tabix": "https://github.com/statgen/localzoom#dbcc3e5",
+    "locuszoom": "0.10.0",
+    "locuszoom-tabix": "https://github.com/statgen/localzoom#918fd75",
     "pako": "^1.0.8",
     "underscore": "1.8.3",
     "vue": "^2.6.10",

yarn.lock

@@ -3253,25 +3253,25 @@ locate-path@^3.0.0:
     p-locate "^3.0.0"
     path-exists "^3.0.0"
 
-"locuszoom-tabix@https://github.com/statgen/localzoom#dbcc3e5":
-  version "0.4.0"
-  resolved "https://github.com/statgen/localzoom#dbcc3e59a2061903d831ca4f8d6874f271f2590f"
+"locuszoom-tabix@https://github.com/statgen/localzoom#918fd75":
+  version "0.5.0"
+  resolved "https://github.com/statgen/localzoom#918fd7525f7e14c13dae60dc6f630188b1669c53"
   dependencies:
     "@sentry/browser" "^4.5.2"
     bootstrap "^4.1.3"
     bootstrap-vue "^2.0.0-rc.11"
     gwas-credible-sets "^0.1.0"
-    locuszoom "0.10.0-beta.2"
+    locuszoom "0.10.0"
     lodash "^4.17.11"
     tabix-reader "https://github.com/abought/tabix-reader"
     tabulator-tables "^4.1.4"
     vue "^2.6.10"
     vue-bootstrap-typeahead "^0.2.6"
 
-[email protected]-beta.2:
-  version "0.10.0-beta.2"
-  resolved "https://registry.yarnpkg.com/locuszoom/-/locuszoom-0.10.0-beta.2.tgz#7c007c421ee3c1e39f9adab6612874761bb455c6"
-  integrity sha512-SkyquD7OCPJQcCrFoJxHBlA9/U9CNJb+EE1n+O/jnX5CqiFlPUHHrzi8KzBUPZ25DQHdtCHXM7YE+0imHTrYDg==
+[email protected]:
+  version "0.10.0"
+  resolved "https://registry.yarnpkg.com/locuszoom/-/locuszoom-0.10.0.tgz#7dad2341af6e539f6bbf0878ec1753a521e7c647"
+  integrity sha512-v+g8YKHszmZL7/yJg5EDZhrGS3jlGoP/WTXM0WFjTUi8MrPCADaeutwx/FhkmZtbhtlb+khO+8EYItaaTGEMLg==
   dependencies:
     d3 "3.5.17"
     promise-polyfill "^8.1.3"