Merge pull request #1864 from broadinstitute/development

Release 1.53.0
broadinstitute · Aug 23, 2023 · c32094d · c32094d
2 parents b53f67b + a995ce7
commit c32094d
Show file tree

Hide file tree

Showing 10 changed files with 11,752 additions and 23 deletions.
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -360,7 +360,7 @@ GEM
       ast (~> 2.4.1)
     power_assert (2.0.0)
     public_suffix (5.0.1)
-    puma (5.6.4)
+    puma (5.6.7)
       nio4r (~> 2.0)
     racc (1.7.1)
     rack (2.2.7)

diff --git a/app/javascript/components/visualization/RelatedGenesIdeogram.jsx b/app/javascript/components/visualization/RelatedGenesIdeogram.jsx
@@ -148,8 +148,8 @@ export default function RelatedGenesIdeogram({
 
   const verticalPad = 40 // Total top and bottom padding
 
-  // For Ideogram functionality only available for human
-  const showAdvanced = taxon === 'Homo sapiens'
+  // For Ideogram functionality only available for human and mouse
+  const showAdvanced = ['Homo sapiens', 'Mus musculus'].includes(taxon)
 
   useEffect(() => {
     const ideoConfig = {

diff --git a/app/javascript/lib/validation/chunked-line-reader.js b/app/javascript/lib/validation/chunked-line-reader.js
@@ -28,6 +28,7 @@ export default class ChunkedLineReader {
     this.startTime = Date.now() // start the CSFV timer
     this.updateHasMoreChunks()
     this.updateHasMoreLines()
+    this.textEncoder = new TextEncoder()
   }
 
   /**
@@ -115,7 +116,10 @@ export default class ChunkedLineReader {
       }
     }
     this.currentFragment = null
-    this.nextByteToRead = this.nextByteToRead + chunkString.length
+
+    // Check byte length, not string length, to account for non-ASCII Unicode
+    const chunkByteLength = this.textEncoder.encode(chunkString).length
+    this.nextByteToRead = this.nextByteToRead + chunkByteLength
     if (
       (isLastChunk && this.ignoreLastLine) ||
       (!isLastChunk || chunkString.slice(-1).match(newlineRegex))

diff --git a/lib/study_cleanup_tools.rb b/lib/study_cleanup_tools.rb
@@ -66,7 +66,9 @@ def self.delete_all_orphaned_workspaces(project_name = FireCloudClient::PORTAL_N
     'download-agreement-686b0d44c83659cd70616a3f0874fde5',
     'testing-study-6ec03b371c7cf59262df98424ff516e1',
     'new-study-99f2a94b-f8a6-4efb-aa3b-4ecef24e1dad',
-    'testing-study-jdwjl']
+    'testing-study-jdwjl', 
+    'test-study-06387e09-6661-45b5-bc1b-4fc507bd19ea',
+    'main-validation-study-szzob',]
     workspaces.each do |workspace|
       ws_attr = workspace.dig('workspace')
       ws_name = ws_attr['name']

diff --git a/package.json b/package.json
@@ -24,6 +24,7 @@
     "@reach/router": "^1.3.3",
     "@sentry/react": "^7.54.0",
     "@sentry/tracing": "^7.54.0",
+    "@sentry/vite-plugin": "^2.6.2",
     "@single-cell-portal/igv": "2.6.4-beta.1",
     "@tanstack/react-table": "^8.8.5",
     "@vitejs/plugin-react": "^1.2.0",
@@ -32,7 +33,7 @@
     "core-js": "^3.6.4",
     "exifreader": "4.6.0",
     "fflate": "^0.7.3",
-    "ideogram": "1.42.0",
+    "ideogram": "1.44.0",
     "jquery": "3.5.1",
     "jquery-ui": "1.13.2",
     "morpheus-app": "1.0.18",

diff --git a/test/js/setup-tests.js b/test/js/setup-tests.js
@@ -1,3 +1,5 @@
+import { TextEncoder, TextDecoder } from 'util'
+
 import { configure } from 'enzyme'
 import Adapter from 'enzyme-adapter-react-16'
 // Mock `window.location` with Jest spies and extend expect
@@ -18,6 +20,10 @@ setMockOrigin('https://localhost:3000')
 // convert scrolls to no-ops as otherwise they will error
 global.scrollTo = jest.fn()
 
+// For e.g. tests of client-side file validation (CSFV)
+global.TextEncoder = TextEncoder
+global.TextDecoder = TextDecoder
+
 // Needed for tests that import Plotly
 window.URL.createObjectURL = function() {}
 window.HTMLCanvasElement.prototype.getContext = () => {}