Merge branch 'release/0.9.6'

package.json

@@ -1,6 +1,6 @@
 {
   "name": "localzoom",
-  "version": "0.9.5",
+  "version": "0.9.6",
   "license": "MIT",
   "engines": {
     "node": ">=10.13.0"
@@ -18,24 +18,24 @@
   },
   "dependencies": {
     "@sentry/browser": "^4.5.2",
-    "bootstrap": "^4.4.1",
-    "bootstrap-vue": "^2.21.2",
-    "locuszoom": "git+https://github.com/statgen/locuszoom.git#674d25c",
+    "bootstrap": "^4.6.1",
+    "bootstrap-vue": "2.21.2",
+    "locuszoom": "0.14.0",
     "lodash": "^4.17.11",
     "tabulator-tables": "^4.9.3",
     "vue": "^2.6.14",
     "vue-bootstrap-typeahead": "^0.2.6"
   },
   "devDependencies": {
-    "@babel/plugin-proposal-optional-chaining": "^7.16.0",
+    "@babel/plugin-proposal-optional-chaining": "^7.17.12",
     "@vue/cli-plugin-babel": "^3.0.0",
     "@vue/cli-plugin-eslint": "^3.0.0",
     "@vue/cli-plugin-unit-mocha": "^3.0.0",
     "@vue/cli-service": "^3.0.0",
     "@vue/eslint-config-airbnb": "^4.0.0",
-    "@vue/test-utils": "^1.2.2",
+    "@vue/test-utils": "^1.3.0",
     "autoprefixer": "^9.8.8",
-    "chai": "^4.3.4",
+    "chai": "^4.3.6",
     "source-map-loader": "^0.2.4",
     "vue-template-compiler": "^2.6.14"
   }

src/components/GwasToolbar.vue

@@ -8,8 +8,8 @@ import RegionPicker from './RegionPicker.vue';
 import TabixAdder from './TabixAdder.vue';
 
 import { createStudySources, createStudyLayouts } from '../util/lz-helpers';
+import { MAX_REGION_SIZE } from '../util/constants';
 
-const MAX_REGION_SIZE = 1000000;
 
 export default {
     name: 'GwasToolbar',

src/util/constants.js

@@ -5,6 +5,7 @@ const REGEX_POSITION = /^(?:chr)?(\w+)\s*:\s*(\d+)$/;
 const REGEX_REGION = /^(?:chr)?(\w+)\s*:\s*(\d+)-(\d+)$/;
 
 const DEFAULT_REGION_SIZE = 500000;
+const MAX_REGION_SIZE = 2000000;
 
 // Enum that controls recognized data types, so we can rename/ adjust as needed.
 const DATA_TYPES = Object.freeze({
@@ -15,7 +16,7 @@ const DATA_TYPES = Object.freeze({
 
 export {
     DATA_TYPES,
-    DEFAULT_REGION_SIZE,
+    DEFAULT_REGION_SIZE, MAX_REGION_SIZE,
     REGEX_REGION, REGEX_POSITION,
     PORTAL_API_BASE_URL, LD_SERVER_BASE_URL,
 };

src/util/entity-helpers.js

@@ -36,9 +36,10 @@ function positionToStartRange(position, { region_size = DEFAULT_REGION_SIZE, pad
  * @param {number} [region_size=DEFAULT_REGION_SIZE] If specified, enforces a max region size.
  * @returns {[string, number, number]} [chr, start, end]
  */
-function parseRegion(spec, { region_size = DEFAULT_REGION_SIZE }) {
-    const range_match = spec.match(REGEX_REGION);
-    const single_match = spec.match(REGEX_POSITION);
+function parseRegion(spec, { region_size = DEFAULT_REGION_SIZE } = {}) {
+    const region = spec.replace(/,/g, '');
+    const range_match = region.match(REGEX_REGION);
+    const single_match = region.match(REGEX_POSITION);
     let chr;
     let start;
     let end;

src/util/lz-helpers.js

@@ -5,7 +5,7 @@ import tabixSource from 'locuszoom/esm/ext/lz-tabix-source';
 import intervalTracks from 'locuszoom/esm/ext/lz-intervals-track';
 import lzParsers from 'locuszoom/esm/ext/lz-parsers';
 
-import { PORTAL_API_BASE_URL, LD_SERVER_BASE_URL, DATA_TYPES } from './constants';
+import { PORTAL_API_BASE_URL, LD_SERVER_BASE_URL, DATA_TYPES, MAX_REGION_SIZE } from './constants';
 
 LocusZoom.use(credibleSets);
 LocusZoom.use(tabixSource);
@@ -366,6 +366,7 @@ function getBasicLayout(initial_state = {}, study_panels = [], mods = {}) {
     ];
 
     const extra = Object.assign({
+        max_region_scale: MAX_REGION_SIZE,
         state: initial_state,
         panels,
     }, mods);

tests/unit/entity_helpers.js → tests/unit/entity_helpers.spec.js

@@ -5,42 +5,45 @@ import { parseRegion } from '../../src/util/entity-helpers';
 describe('parseRegion', function () {
     it('parses a single position', function () {
         let result = parseRegion('1:1000', {region_size: 100});
-        assert.deepEqual(result, {chr: '1', start: 900, end: 1100}, 'Single position is center of a defined region size');
+        assert.deepEqual(result, {chr: '1', start: 950, end: 1050}, 'Single position is center of a defined region size');
 
         result = parseRegion('chr1:1000', {region_size: 100});
-        assert.deepEqual(result, {chr: '1', start: 900, end: 1100}, 'Allows matching with a leading chr prefix');
+        assert.deepEqual(result, {chr: '1', start: 950, end: 1050}, 'Allows matching with a leading chr prefix');
 
         result = parseRegion('1:10', {region_size: 100});
-        assert.deepEqual(result, {chr: '1', start: 1, end: 110}, 'Single position is center of a defined region size, and respects minima');
+        assert.deepEqual(result, {chr: '1', start: 1, end: 60}, 'Single position is inside a defined region size, and respects minima');
     });
 
     it('fails on totally unrecognized formats', function () {
-        assert.throws(() => parseRegion('TCF7L2'), 'Invalid format because not a region', /Could not parse/);
-        assert.throws(() => parseRegion('1:23ab'), 'Invalid format because trailing chars', /Could not parse/);
+        assert.throws(() => parseRegion('TCF7L2'), /Could not parse/);
+        assert.throws(() => parseRegion('1:23ab'), /Could not parse/);
     });
 
     it('handles various region types', function () {
         // Note: this region is actually too small for a real LZ plot, but that is not the job of this function to handle.
-        let result = parseRegion('1:1000-2000', {region_size: 100});
-        assert.deepEqual(result, {chr: '1', start: 1000, end: 1000}, 'Faithfully parses a region as given');
+        let result = parseRegion('1:1000-2000', {region_size: 1000});
+        assert.deepEqual(result, {chr: '1', start: 1000, end: 2000}, 'Faithfully parses a region as given');
 
-        result = parseRegion('chr1:1000-2000', {region_size: 100});
-        assert.deepEqual(result, {chr: '1', start: 1000, end: 1000}, 'Allows matching with a leading chr prefix');
+        result = parseRegion('chr1:1000-2000', {region_size: 1000});
+        assert.deepEqual(result, {chr: '1', start: 1000, end: 2000}, 'Allows matching with a leading chr prefix');
+
+        result = parseRegion('chr1:1,000-2,000', {region_size: 1000});
+        assert.deepEqual(result, {chr: '1', start: 1000, end: 2000}, 'Allows matching regions with commas');
 
         assert.throws(
             () => parseRegion('2:1-1000', {region_size: 250}),
+            /Maximum allowable/,
             'Warns if the requested region is too wide',
-            /Maximum allowable/
         );
         assert.throws(
             () => parseRegion('2:1000-1', {region_size: 250}),
+            /smaller than/,
             'Warns if the requested region makes no sense',
-            /smaller than/
         );
         assert.throws(
             () => parseRegion('chr1:1000-2000ab', {region_size: 250}),
+            /Could not parse/,
             'Fails because trailing characters are present',
-            /Could not parse/
         );
     });
 });