chore: staging deploy; 9/20/22 (#457)

* Updating explorer to appropriately handle upgraded CXGs (#431) * update explorer to use two X arrays * update for backwards compatibility * bug fix * fix accidental recursion * fix shape return * more fixes to backwards compatibility * black * black * update to use attr(0) for unit tests failing due to anonymous attr name * refactor row array name * make use for dictionary encoded obs array * update query_obs_array * update query_obs_array * fix_typo * black * fix faulty except block * remaster pbmc3k.cxg obs array * remaster * black * black p2 * revert * update docs * revert * update docs * revise not mandatory * add comment * clearer arg * remove param from docstring * version update * update arg usage to colwise * add clause * update tests with sparse data fixture * black * update tests * update tests * combine more tests with subtests Co-authored-by: atarashansky <atarashansky@czimacos3990.lan> Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.hsd1.ma.comcast.net> Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.local> * Upgrade Flask and other server python dependencies (#438) * wip * wip * wip * revert push_tests branch change Co-authored-by: Mike Lin <mlin@CZIMACOS3726.hawaii.rr.com> Co-authored-by: atarashansky <atarashansky@chanzuckerberg.com> * bug fix (#446) Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.hsd1.ma.comcast.net> * Added the data portal navigation bar to explorer (#382) * added unified navbar * clean up * updates * remove Roboto declaration * remove Embedding and Autosave * remove home from dataset selector and move it to the bottom - add dropdown to help * fix lint * fix: SVG import * upgrade node version * add Roboto Condensed * fix: add back code change dropped from resolving merge conflicts * chore: update package-lock.json * fix: ts lint * update test * update test Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.local> Co-authored-by: Timmy Huang <thuang@chanzuckerberg.com> * chore(node): Upgrade to 16 in Dockerfile (#448) * update doc version (#447) Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.hsd1.ma.comcast.net> * fix(navbar): WMG link (#449) * fix edge case where categories dont exist for categoricals (#450) Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.local> * chore: Add server timings to gene expression API routes (#451) * add server timing to dataset query and encode * add server timing to dataset query and encode * remove f strings Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.hsd1.ma.comcast.net> * fix timing (#452) Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.local> * revert mapColumns to default behavior. engineers are now responsible for handling dict encoded arrays in the callback (#454) Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.hsd1.ma.comcast.net> Co-authored-by: atarashansky <atarashansky@chanzuckerberg.com> Co-authored-by: atarashansky <atarashansky@czimacos3990.lan> Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.hsd1.ma.comcast.net> Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.local> Co-authored-by: Mike Lin <mlin@mlin.net> Co-authored-by: Mike Lin <mlin@CZIMACOS3726.hawaii.rr.com> Co-authored-by: Timmy Huang <thuang@chanzuckerberg.com> Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>
chanzuckerberg · Sep 20, 2022 · f1615ec · f1615ec
1 parent 987a8c5
commit f1615ec
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Showing 121 changed files with 10,246 additions and 4,980 deletions.
diff --git a/client/.nvmrc b/client/.nvmrc
@@ -0,0 +1 @@
+v16
diff --git a/client/__tests__/e2e/__snapshots__/e2e.test.ts.snap b/client/__tests__/e2e/__snapshots__/e2e.test.ts.snap
diff --git a/client/__tests__/e2e/cellxgeneActions.ts b/client/__tests__/e2e/cellxgeneActions.ts
@@ -30,6 +30,7 @@ export async function drag(testId: any, start: any, end: any, lasso = false) {
   const y2 = elBox.content[0].y + end.y;
   await page.mouse.move(x1, y1);
   await page.mouse.down();
+
   if (lasso) {
     await page.mouse.move(x2, y1);
     await page.mouse.move(x2, y2);
@@ -38,6 +39,7 @@ export async function drag(testId: any, start: any, end: any, lasso = false) {
   } else {
     await page.mouse.move(x2, y2);
   }
+
   await page.mouse.up();
 }
 

diff --git a/client/__tests__/e2e/data.ts b/client/__tests__/e2e/data.ts
@@ -27,7 +27,7 @@ export const datasets = {
       lasso: [
         {
           "coordinates-as-percent": { x1: 0.1, y1: 0.25, x2: 0.7, y2: 0.75 },
-          count: "1131",
+          count: "1094",
         },
       ],
       categorical: [
@@ -83,7 +83,7 @@ export const datasets = {
           values: ["B cells", "Megakaryocytes"],
         },
       ],
-      count: "357",
+      count: "332",
       categorical: {
         louvain: {
           "B cells": "342",
@@ -98,14 +98,14 @@ export const datasets = {
       },
       lasso: {
         "coordinates-as-percent": { x1: 0.25, y1: 0.05, x2: 0.75, y2: 0.55 },
-        count: "332",
+        count: "357",
       },
     },
     scatter: {
       genes: { x: "S100A8", y: "FCGR3A" },
     },
     pan: {
-      "coordinates-as-percent": { x1: 0.75, y1: 0.75, x2: 0.35, y2: 0.35 },
+      "coordinates-as-percent": { x1: 0.75, y1: 0.75, x2: 0.25, y2: 0.25 },
     },
     features: {
       panzoom: {

diff --git a/client/__tests__/e2e/e2e.test.ts b/client/__tests__/e2e/e2e.test.ts
@@ -350,17 +350,20 @@ describe("graph overlay", () => {
       `${categoryValue}-centroid-label`
     );
 
-    await drag("layout-graph", panCoords.start, panCoords.end, false);
-    const terminalCoordinates = await getElementCoordinates(
-      `${categoryValue}-centroid-label`
-    );
+    await tryUntil(async () => {
+      await drag("layout-graph", panCoords.start, panCoords.end, false);
 
-    expect(terminalCoordinates[0] - initialCoordinates[0]).toBeCloseTo(
-      panCoords.end.x - panCoords.start.x
-    );
-    expect(terminalCoordinates[1] - initialCoordinates[1]).toBeCloseTo(
-      panCoords.end.y - panCoords.start.y
-    );
+      const terminalCoordinates = await getElementCoordinates(
+        `${categoryValue}-centroid-label`
+      );
+
+      expect(terminalCoordinates[0] - initialCoordinates[0]).toBeCloseTo(
+        panCoords.end.x - panCoords.start.x
+      );
+      expect(terminalCoordinates[1] - initialCoordinates[1]).toBeCloseTo(
+        panCoords.end.y - panCoords.start.y
+      );
+    });
   });
 });
 

diff --git a/client/configuration/webpack/SUPPORTED_BROWSERS_REGEX.js b/client/configuration/webpack/SUPPORTED_BROWSERS_REGEX.js
diff --git a/client/configuration/webpack/webpack.config.dev.js b/client/configuration/webpack/webpack.config.dev.js
@@ -27,7 +27,10 @@ const devConfig = {
   output: {
     pathinfo: true,
     filename: "static/js/bundle.js",
-    publicPath: "/", // ensures the static asset calls use "/" as the root and not "/<base_url>/<dataset>"
+    // (thuang): This is needed to make sure static asset url path is '/static/assets/',
+    // so it ignores the base_url (/d, /e) and dataset in the url.
+    // e.g., http://localhost:3000/static/assets/heatmap.svg
+    publicPath: "/",
   },
   module: {
     rules: [
@@ -39,7 +42,6 @@ const devConfig = {
       {
         test: /\.(jpg|png|gif|eot|svg|ttf|woff|woff2|otf)$/i,
         loader: "file-loader",
-        include: [nodeModules, fonts],
         options: {
           name: "static/assets/[name].[ext]",
           // (thuang): This is needed to make sure @font url path is '/static/assets/'

diff --git a/client/configuration/webpack/webpack.config.prod.js b/client/configuration/webpack/webpack.config.prod.js
@@ -56,11 +56,8 @@ const prodConfig = {
       {
         test: /\.(jpg|png|gif|eot|svg|ttf|woff|woff2|otf)$/i,
         loader: "file-loader",
-        include: [nodeModules, fonts],
         options: {
           name: "static/assets/[name]-[contenthash].[ext]",
-          // (thuang): This is needed to make sure @font url path is '../static/assets/'
-          publicPath: "..",
         },
       },
     ],

diff --git a/client/index.html b/client/index.html
@@ -20,19 +20,27 @@
       label,
       text,
       div {
-        font-family: "Roboto Condensed", "Helvetica Neue", "Helvetica", "Arial", sans-serif;
+        font-family: "Roboto Condensed", "Helvetica Neue", "Helvetica", "Arial",
+          sans-serif;
         font-size: 14px;
         letter-spacing: -0.006em;
       }
       body {
         margin: 0;
         padding: 0;
+        -webkit-font-smoothing: antialiased;
       }
 
       * {
         box-sizing: border-box;
       }
     </style>
+    <link rel="preconnect" href="https://fonts.googleapis.com" />
+    <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin />
+    <link
+      href="https://fonts.googleapis.com/css2?family=Roboto+Condensed:ital,wght@0,400;0,700;1,400&display=swap"
+      rel="stylesheet"
+    />
   </head>
   <body>
     <script type="text/javascript">