Merge branch 'release/0.9.3'

statgen · Dec 10, 2021 · 83f5181 · 83f5181
2 parents 8b1364f + bf3a620
commit 83f5181
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Showing 5 changed files with 25 additions and 11 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "localzoom",
-  "version": "0.9.2",
+  "version": "0.9.3",
   "license": "MIT",
   "engines": {
     "node": ">=10.13.0"

diff --git a/src/App.vue b/src/App.vue
@@ -42,6 +42,11 @@ export default {
             has_credible_sets: true,
         };
     },
+    computed: {
+        show_instructions() {
+            return window.location.hash.includes('instructions');
+        },
+    },
     methods: {
         receiveTrackOptions(data_type, filename, display_name, source_configs, panel_configs, extra_plot_state) {
             if (!this.known_tracks.length) {
@@ -95,6 +100,7 @@ export default {
           class="btn btn-link">Instructions</button>
         <b-collapse
           id="instructions"
+          :visible="show_instructions"
           class="mt-1 mb-4">
           <b-card>
             <div class="card-text">
@@ -122,9 +128,9 @@ export default {
                     <li>The data is hosted in a place that is reachable by web browser (eg local files
                     or a service such as S3)
                     </li>
-                    <li>If using a remote URL, the host location must support byte range requests. (<a
+                    <li>If using a remote URL, the host location must support cross-origin byte range requests. (<a
                       href="https://developer.mozilla.org/en-US/docs/Web/HTTP/Range_requests#Checking_if_a_server_supports_partial_requests">how
-                      to check</a>)
+                      to check</a>) (<a href="https://docs.cancergenomicscloud.org/docs/enabling-cross-origin-resource-sharing-cors#CORS">how to configure cloud storage</a>)
                     </li>
                     <li>Your file contains all of the information required to draw a plot (see individual file format instructions for details).</li>
                   </ol>

diff --git a/src/components/GwasToolbar.vue b/src/components/GwasToolbar.vue
@@ -22,7 +22,6 @@ export default {
         TabixAdder,
     },
     props: {
-        // These two fields are sync bindings (this component notifies its parent of changes)
         genome_build: {
             type: String,
             default: 'GRCh37',
@@ -37,11 +36,13 @@ export default {
             default: 6,
         },
         // Track a list of studies that were added to the plot. Useful to prevent duplicates.
-        // TODO: move to live-binding provide/inject to support export widget / my.locuszoom.org ?
         known_tracks: {
             type: Array,
             default: () => [], // Each item is object of form { type, filename, display_name }
         },
+        // Get a list of suggested entries for batch mode (useful in my.locuszoom.org, which pre-calculates top loci genome wide)
+        //  Should fetch pre-computed top loci, and return list of [ {chr, start, end} ] entries
+        batch_region_getter: { type: Function, default: null },
     },
     data() {
         return {
@@ -146,8 +147,6 @@ export default {
             @ready="receiveTabixReader"
             @fail="showMessage"
           />
-
-
         </div>
       </div>
       <div
@@ -165,7 +164,11 @@ export default {
           <batch-spec
             :max_range="max_region_size"
             class="ml-1"
-            @ready="activateBatchMode"/>
+            @ready="activateBatchMode">
+            <template v-if="batch_region_getter" #preset-button="{updateRegions}">
+              <button class="btn btn-warning" @click="updateRegions(batch_region_getter())">Get top hits</button>
+            </template>
+          </batch-spec>
         </div>
         <b-dropdown
           v-else

diff --git a/src/components/TabixAdder.vue b/src/components/TabixAdder.vue
@@ -9,11 +9,13 @@ import { blobReader, urlReader } from 'tabix-reader';
 import GwasParserOptions from './GwasParserOptions.vue';
 import { DATA_TYPES } from '../util/constants';
 import { positionToStartRange } from '../util/entity-helpers';
+import { VBTooltip } from 'bootstrap-vue/src/';
 
 
 export default {
     name: 'TabixAdder',
     components: { BDropdown, BFormGroup, BFormRadio, BFormRadioGroup, GwasParserOptions },
+    directives: { VBTooltip },
     props: {
         // Allow the user to add custom LD
         allow_ld: { type: Boolean, default: false },
@@ -230,9 +232,12 @@ export default {
     <b-dropdown
       ref="options_dropdown"
       :lazy="true"
-      text="Add tabix-indexed datafile"
       variant="success"
     >
+      <template #button-content>
+        <span v-v-b-tooltip.right="'This will plot data from local files. Nothing will be uploaded and these tracks will disappear when the page reloads.'">Add tabix-indexed datafile</span>
+      </template>
+
       <div
         class="px-3"
         style="width: 300px;">
@@ -295,7 +300,7 @@ export default {
               name="data-type"
               value="plink_ld"
             >
-              PLINK 1.9 LD (overlay on GWAS; see guide above)
+              PLINK 1.9 LD (overlay on GWAS; see <a target="_blank" href="https://statgen.github.io/localzoom#instructions">instructions</a>)
             </b-form-radio>
           </b-form-group>