Merge pull request #28 from galaxyproject/fran/16-merge-website-catalog

data-catalog/.env → .env

@@ -1,3 +1,3 @@
 NEXT_PUBLIC_SITEMAP_DOMAIN='https://brc-analytics.dev.clevercanary.com'
-NEXT_PUBLIC_BASE_PATH='/data'
-SITEMAP_EXCLUDE='/export*,/login'
+NEXT_PUBLIC_BASE_PATH=''
+SITEMAP_EXCLUDE='/export*,/login'

data-catalog/.eslintignore → .eslintignore

@@ -1,6 +1,5 @@
 **/node_modules/*
+**/out/*
 **/.next/*
 
-/out
-
 venv

.github/workflows/run-checks.yml

@@ -10,12 +10,6 @@ jobs:
         with:
           node-version: "20.10.0"
       - run: |
-          cd ./website
-          npm ci
-          npm run check-format
-          npm run lint
-          npx tsc --noEmit
-          cd ../data-catalog
           npm ci
           npm run check-format
           npm run lint

.gitignore

@@ -1,4 +1,36 @@
 # dependencies
 /node_modules
 
-.idea/
+# next.js
+/.next/
+
+# misc
+.DS_Store
+*.pem
+
+# debug
+npm-debug.log*
+
+# env files
+/.env*.local
+/.env.development
+/.env.production
+
+# typescript
+*.tsbuildinfo
+
+# editors
+/.vscode
+.idea
+
+# nvm
+.nvmrc
+
+# favicons
+/public/favicons/*
+
+# Build Dir
+/out
+
+# python
+venv

.husky/pre-commit

@@ -3,33 +3,24 @@
 
 echo '🏗️👷 Checking your project before committing'
 
-for app in "website" "data-catalog"
-do
-    echo "\nChecking $app"
+# Check Prettier
+npm run check-format ||
+(
+    echo '🤔 Prettier Check Failed. Run npx prettier --write . try commit again.';
+    false;
+)
 
-    cd "./$app"
-
-    # Check Prettier
-    npm run check-format ||
-    (
-        echo '🤔 Prettier Check Failed. Run npx prettier --write . try commit again.';
-        false;
-    )
-
-    # Check ESLint
-    npm run lint ||
-    (
-            echo '🤔  ESLint Check Failed. Make the required changes listed above, add changes and try to commit again.'
-            false; 
-    )
-
-    # Check TypeScript
-    npx tsc --noEmit ||
-    (
-        echo 'TypeScript compile failed';
+# Check ESLint
+npm run lint ||
+(
+        echo '🤔  ESLint Check Failed. Make the required changes listed above, add changes and try to commit again.'
         false;
-    )
-    echo 'TypeScript compile succeeded!'
+)
 
-    cd ..
-done
+# Check TypeScript
+npx tsc --noEmit ||
+(
+	echo 'TypeScript compile failed';
+	false;
+)
+echo 'TypeScript compile succeeded!'

data-catalog/.prettierignore → .prettierignore

@@ -5,7 +5,7 @@
 node_modules
 
 # build
-/out
+out
 
 # python
 venv

README.md

@@ -1 +1,22 @@
-# brc-analytics
+# brc-analytics
+
+# BRC Analytics Data Catalog
+
+## Building the data source files
+
+Create a Python virtual environment and install requirements:
+
+```shell
+python3 -m venv ./venv
+source ./venv/bin/activate
+pip install -r ./files/requirements.txt
+```
+
+Then run the script:
+
+```shell
+python3 ./files/build-genomes-files.py
+```
+
+The environment can be deactivated by running `deactivate`, and re-activated by running `source ./venv/bin/activate`
+again.

website/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx → app/components/Home/components/Section/components/SectionHero/sectionHero.tsx

@@ -1,5 +1,5 @@
-import { ButtonPrimary } from "@databiosphere/findable-ui/lib/components/common/Button/components/ButtonPrimary/buttonPrimary";
-import { ROUTES } from "../../../../../../routes/constants";
+import { Button } from "@mui/material";
+import { ROUTES } from "../../../../../../../routes/constants";
 import {
   Head,
   Headline,
@@ -27,7 +27,9 @@ export const SectionHero = (): JSX.Element => {
               annotations and functional insights into disease-causing organisms
               and their carriers
             </Subhead>
-            <ButtonPrimary href={ROUTES.GET_STARTED}>Get Started</ButtonPrimary>
+            <Button color="hero" href={ROUTES.GENOMES} variant="contained">
+              Get Started
+            </Button>
           </SubHeadlinePositioner>
         </SubHeadline>
       </SectionLayout>

data-catalog/app/components/Table/components/TableCell/components/AnalyzeGenome/analyzeGenome.tsx → app/components/Table/components/TableCell/components/AnalyzeGenome/analyzeGenome.tsx

@@ -4,7 +4,7 @@ import {
 } from "@databiosphere/findable-ui/lib/components/Links/common/entities";
 import { Button, Tooltip } from "@mui/material";
 import Router from "next/router";
-import { ROUTES } from "../../../../../../../routes/contants";
+import { ROUTES } from "../../../../../../../routes/constants";
 import { BRCDataCatalogGenome } from "../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
 import { AnalyzeGenomeIcon } from "../../../../../common/CustomIcon/components/AnalyzeGenomeIcon/analyzeGenomeIcon";
 import { ViewGenomeIcon } from "../../../../../common/CustomIcon/components/ViewGenomeIcon/viewGenomeIcon";

data-catalog/app/components/index.ts → app/components/index.ts

@@ -17,9 +17,11 @@ export {
   BackPageContentSideColumn,
   BackPageContentSingleColumn,
 } from "@databiosphere/findable-ui/lib/components/Layout/components/BackPage/backPageView.styles";
+export { Logo } from "@databiosphere/findable-ui/lib/components/Layout/components/Header/components/Content/components/Logo/logo";
 export { Link } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link";
 export { BasicCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/BasicCell/basicCell";
 export { AnalysisMethod } from "./Entity/components/AnalysisMethod/analysisMethod";
 export { AnalysisPortals } from "./Entity/components/AnalysisPortals/analysisPortals";
 export { DetailViewHero } from "./Layout/components/Detail/components/DetailViewHero/detailViewHero";
+export { Branding } from "./Layout/components/Footer/components/Branding/branding";
 export { AnalyzeGenome } from "./Table/components/TableCell/components/AnalyzeGenome/analyzeGenome";

website/app/config/config.ts → app/config/config.ts

@@ -1,8 +1,9 @@
 import { setConfig } from "@databiosphere/findable-ui/lib/config/config";
 import { SiteConfig } from "@databiosphere/findable-ui/lib/config/entities";
-import brcAnalyticsSiteLocal from "../../site-config/brc-analytics-site/local/config";
+import brcAnalyticsLocal from "../../site-config/brc-analytics/local/config";
+
 const CONFIGS: { [k: string]: SiteConfig } = {
-  "brc-analytics-site-local": brcAnalyticsSiteLocal,
+  "brc-analytics-local": brcAnalyticsLocal,
 };
 
 let appConfig: SiteConfig | null = null;

website/app/theme/common/components.ts → app/theme/common/components.ts

@@ -8,22 +8,25 @@ import { Components, Theme } from "@mui/material";
  */
 export const MuiButton = (theme: Theme): Components["MuiButton"] => {
   return {
-    styleOverrides: {
-      containedPrimary: {
-        boxShadow: `0px 1px 0px 0px rgba(0, 0, 0, 0.08), 0px -1px 0px 0px rgba(0, 0, 0, 0.20) inset`,
-        // TODO(cc): update theme MuiButton "active" state.
-        // eslint-disable-next-line sort-keys -- disabling key order for readability
-        "&:active": {
-          backgroundColor: theme.palette.primary.main,
-          boxShadow: `0px -1px 0px 0px rgba(0, 0, 0, 0.20) inset`,
-        },
-        // TODO(cc): update theme MuiButton "hover" state.
-        "&:hover": {
-          backgroundColor: theme.palette.primary.main,
+    variants: [
+      {
+        props: { color: "hero", variant: "contained" },
+        style: {
           boxShadow: `0px 1px 0px 0px rgba(0, 0, 0, 0.08), 0px -1px 0px 0px rgba(0, 0, 0, 0.20) inset`,
+          color: theme.palette.common.white,
+          // eslint-disable-next-line sort-keys -- disabling key order for readability
+          "&:hover": {
+            backgroundColor: theme.palette.hero.main,
+            boxShadow: `0px 1px 0px 0px rgba(0, 0, 0, 0.08), 0px -1px 0px 0px rgba(0, 0, 0, 0.20) inset`,
+          },
+          // eslint-disable-next-line sort-keys -- disabling key order for readability
+          "&:active": {
+            backgroundColor: theme.palette.hero.main,
+            boxShadow: "none",
+          },
         },
       },
-    },
+    ],
   };
 };
 

app/theme/common/palette.ts

@@ -0,0 +1,23 @@
+import { PaletteColorOptions } from "@mui/material";
+
+/**
+ * Palette "Hero"
+ */
+enum HERO {
+  LIGHT = "#28285B",
+  MAIN = "#28285B",
+}
+
+/**
+ * Color constants
+ */
+export const heroLight = HERO.LIGHT;
+export const heroMain = HERO.MAIN;
+
+/**
+ * Palette Option "Hero"
+ */
+export const hero: PaletteColorOptions = {
+  light: heroLight,
+  main: heroMain,
+};

website/app/theme/theme.ts → app/theme/theme.ts

@@ -1,6 +1,7 @@
 import { createTheme, Theme } from "@mui/material";
 import { deepmerge } from "@mui/utils";
 import * as C from "./common/components";
+import * as P from "./common/palette";
 
 /**
  * Returns BRC customized theme.
@@ -14,6 +15,9 @@ export function mergeAppTheme(theme: Theme): Theme {
         MuiButton: C.MuiButton(theme),
         MuiCssBaseline: C.MuiCssBaseline(theme),
       },
+      palette: {
+        hero: P.hero,
+      },
     })
   );
 }

data-catalog/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts → app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts

@@ -5,9 +5,9 @@ import {
   Value,
 } from "@databiosphere/findable-ui/lib/components/common/KeyValuePairs/keyValuePairs";
 import { ComponentProps } from "react";
-import { ROUTES } from "../../../../../routes/contants";
+import { ROUTES } from "../../../../../routes/constants";
 import { BRCDataCatalogGenome } from "../../../../apis/catalog/brc-analytics-catalog/common/entities";
-import * as C from "../../../../components/index";
+import * as C from "../../../../components";
 import { GENOME_BROWSER } from "./constants";
 
 /**

website/cc-brc-analytics.dev.clevercanary.com-deploy.sh → cc-brc-analytics.dev.clevercanary.com-build.sh

@@ -1,20 +1,20 @@
 #!/usr/bin/env bash
-
 # Exit immediately if a command exits with a non-zero status
 set -e
 
 echo \"Deleting ./out/\"
 rm -rf ./out
 
+# install node version 20.10.0
 n 20.10.0
 npm ci
+export NEXT_PUBLIC_BASE_PATH=""
 
-
-# Build the website
+# Build catalog
 npm run build:local
 
 export BUCKET=s3://tik-brc-analytics.dev/
 export SRCDIR=out/
 
 aws s3 sync  $SRCDIR $BUCKET --delete --profile excira
-aws cloudfront create-invalidation --distribution-id E1OF5ESEGD5VAG --paths "/*" --profile excira
+aws cloudfront create-invalidation --distribution-id E1OF5ESEGD5VAG --paths "/*" --profile excira