feat: set up basic website and catalog apps (#4) (#11)

* chore: add gitignore and package jsons for website (4)

* feat: set up minimal website (#4)

* chore: remove unnecessary commitlint dependency (#4)

* chore: add commit message checks (#4)

* chore: add pre-commit checks (#4)

* chore: add github action to run checks on pull request (#4)

* feat: set up minimal catalog (#4)

* chore: update precommit hook to check both apps (#4)

* chore: update github action to check both apps (#4)

* fix: add blank favicons (#4)

* chore: use latest version of findable ui (#4)

* Fix PUBLIC_DIR creation when run in a new repo -- public won't exist and
we need to create /public/ as well as /public/favicons/

---------

Co-authored-by: Dannon Baker <[email protected]>

.github/workflows/run-checks.yml

@@ -0,0 +1,22 @@
+name: Run checks
+on: [pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-node@v2
+        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
+          npx tsc --noEmit

.gitignore

@@ -0,0 +1,2 @@
+# dependencies
+/node_modules

.husky/commit-msg

@@ -0,0 +1,18 @@
+#!/usr/bin/env sh
+. "$(dirname -- "$0")/_/husky.sh"
+
+echo "Checking commit message"
+
+# Check for issue number
+
+commit_regex='#[0-9]'
+error_msg="Aborting commit. Your commit message is missing a '#xxx' reference to a corresponding GitHub issue. Add '--no-verify' to your git commit command if you wish to skip this check."
+
+if ! grep -iqE "$commit_regex" "$1"; then
+    echo "$error_msg" >&2
+    exit 1
+fi
+
+# Check for Conventional Commits format
+
+npx commitlint --config ./commitlint.config.js --edit $1

.husky/pre-commit

@@ -0,0 +1,35 @@
+#!/bin/sh
+. "$(dirname "$0")/_/husky.sh"
+
+echo '🏗️👷 Checking your project before committing'
+
+for app in "website" "data-catalog"
+do
+    echo "\nChecking $app"
+
+    cd "./$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';
+        false;
+    )
+    echo 'TypeScript compile succeeded!'
+
+    cd ..
+done

commitlint.config.js

@@ -0,0 +1 @@
+module.exports = { extends: ["@commitlint/config-conventional"] };

data-catalog/.eslintignore

@@ -0,0 +1,2 @@
+**/node_modules/*
+**/.next/*

data-catalog/.eslintrc.json

@@ -0,0 +1,71 @@
+{
+  "parser": "@typescript-eslint/parser",
+  "plugins": [
+    "@typescript-eslint",
+    "sonarjs",
+    "jsdoc",
+    "sort-destructure-keys",
+    "typescript-sort-keys",
+    "react-hooks"
+  ],
+  "extends": [
+    "eslint:recommended",
+    "plugin:@typescript-eslint/recommended",
+    "prettier",
+    "plugin:prettier/recommended",
+    "next",
+    "plugin:sonarjs/recommended",
+    "plugin:eslint-comments/recommended"
+  ],
+  "rules": {
+    "sort-keys": [
+      "error",
+      "asc",
+      {
+        "caseSensitive": true,
+        "minKeys": 2,
+        "natural": false
+      }
+    ],
+    "sort-destructure-keys/sort-destructure-keys": [
+      "error",
+      {
+        "caseSensitive": false
+      }
+    ],
+    "typescript-sort-keys/interface": [
+      "error",
+      "asc",
+      {
+        "caseSensitive": false
+      }
+    ],
+    "typescript-sort-keys/string-enum": [
+      "error",
+      "asc",
+      {
+        "caseSensitive": false
+      }
+    ],
+    "eslint-comments/require-description": "error",
+    "jsdoc/require-description": "error",
+    "jsdoc/require-param": "error",
+    "jsdoc/require-param-name": "error",
+    "jsdoc/require-param-description": "error",
+    "jsdoc/require-hyphen-before-param-description": "error",
+    "jsdoc/require-returns": "error",
+    "jsdoc/require-returns-description": "error",
+    "jsdoc/check-alignment": "error",
+    "jsdoc/check-param-names": "error",
+    "react-hooks/exhaustive-deps": "error"
+  },
+  "overrides": [
+    {
+      "files": "**",
+      "excludedFiles": "*.styles.ts?(x)",
+      "rules": {
+        "@typescript-eslint/explicit-function-return-type": "error"
+      }
+    }
+  ]
+}

data-catalog/.gitignore

@@ -0,0 +1,30 @@
+# dependencies
+/node_modules
+
+# 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/*

data-catalog/.prettierignore

@@ -0,0 +1,5 @@
+# next.js
+.next
+
+# dependencies
+node_modules

data-catalog/.prettierrc.json

@@ -0,0 +1 @@
+{}

data-catalog/app/apis/catalog/brc-analytics-catalog/common/entities.ts

@@ -0,0 +1,3 @@
+export interface BRCDataCatalogGenome {
+  species: string;
+}

data-catalog/app/components/index.ts

@@ -0,0 +1 @@
+export { BasicCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/BasicCell/basicCell";

data-catalog/app/config/config.ts

@@ -0,0 +1,31 @@
+import { setConfig } from "@databiosphere/findable-ui/lib/config/config";
+import { SiteConfig } from "@databiosphere/findable-ui/lib/config/entities";
+import brcAnalyticsCatalogLocal from "../../site-config/brc-analytics-catalog/local/config";
+const CONFIGS: { [k: string]: SiteConfig } = {
+  "brc-analytics-catalog-local": brcAnalyticsCatalogLocal,
+};
+
+let appConfig: SiteConfig | null = null;
+
+export const config = (): SiteConfig => {
+  if (appConfig) {
+    return appConfig;
+  }
+
+  const config = process.env.NEXT_PUBLIC_SITE_CONFIG;
+
+  if (!config) {
+    console.error(`Config not found. config: ${config}`);
+  }
+
+  appConfig = CONFIGS[config as string];
+
+  if (!appConfig) {
+    console.error(`No app config was found for the config: ${config}`);
+  } else {
+    console.log(`Using app config ${config}`);
+  }
+
+  setConfig(appConfig); // Sets app config.
+  return appConfig;
+};

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

@@ -0,0 +1,15 @@
+import { BRCDataCatalogGenome } from "../../../../apis/catalog/brc-analytics-catalog/common/entities";
+import * as C from "../../../../components/index";
+
+/**
+ * Build props for the species cell.
+ * @param genome - Genome entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildSpecies = (
+  genome: BRCDataCatalogGenome
+): React.ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: genome.species,
+  };
+};

data-catalog/files/out/genomes.json

@@ -0,0 +1 @@
+[{ "species": "Foo bar" }]

data-catalog/next-env.d.ts

@@ -0,0 +1,6 @@
+/// <reference types="next" />
+/// <reference types="next/image-types/global" />
+/// <reference types="next/navigation-types/compat/navigation" />
+
+// NOTE: This file should not be edited
+// see https://nextjs.org/docs/basic-features/typescript for more information.

data-catalog/next.config.mjs

@@ -0,0 +1,83 @@
+import nextMDX from "@next/mdx";
+import withPlugins from "next-compose-plugins";
+import path from "path";
+
+const ESM_PACKAGES = [
+  "axios",
+  "@databiosphere/findable-ui",
+  "@tanstack/react-table",
+];
+
+const withMDX = nextMDX({
+  extension: /\.mdx?$/,
+});
+export default withPlugins(
+  [[withMDX, { pageExtensions: ["md", "mdx", "ts", "tsx"] }]],
+  {
+    basePath: "",
+    experimental: {
+      instrumentationHook: true,
+    },
+    images: {
+      unoptimized: true,
+    },
+    reactStrictMode: true,
+    transpilePackages: [...ESM_PACKAGES],
+    webpack: (config) => {
+      // Add the alias for the peer dependency
+      config.resolve.alias["@emotion/react"] = path.resolve(
+        process.cwd(),
+        "node_modules/@emotion/react"
+      );
+      config.resolve.alias["@emotion/styled"] = path.resolve(
+        process.cwd(),
+        "node_modules/@emotion/styled"
+      );
+      config.resolve.alias["@mui/icons-material"] = path.resolve(
+        process.cwd(),
+        "node_modules/@mui/icons-material"
+      );
+      config.resolve.alias["@mui/material"] = path.resolve(
+        process.cwd(),
+        "node_modules/@mui/material"
+      );
+      config.resolve.alias["react-dropzone"] = path.resolve(
+        process.cwd(),
+        "node_modules/react-dropzone"
+      );
+      config.resolve.alias["isomorphic-dompurify"] = path.resolve(
+        process.cwd(),
+        "node_modules/isomorphic-dompurify"
+      );
+      config.resolve.alias["next"] = path.resolve(
+        process.cwd(),
+        "node_modules/next"
+      );
+      config.resolve.alias["react"] = path.resolve(
+        process.cwd(),
+        "node_modules/react"
+      );
+      config.resolve.alias["react-dom"] = path.resolve(
+        process.cwd(),
+        "node_modules/react-dom"
+      );
+      config.resolve.alias["react-gtm-module"] = path.resolve(
+        process.cwd(),
+        "node_modules/react-gtm-module"
+      );
+      config.resolve.alias["react-window"] = path.resolve(
+        process.cwd(),
+        "node_modules/react-window"
+      );
+      config.resolve.alias["uuid"] = path.resolve(
+        process.cwd(),
+        "node_modules/uuid"
+      );
+      config.resolve.alias["validate.js"] = path.resolve(
+        process.cwd(),
+        "node_modules/validate.js"
+      );
+      return config;
+    },
+  }
+);