feat(init): Initial release.

.editorconfig

@@ -0,0 +1,13 @@
+# editorconfig.org
+root = true
+
+[*]
+indent_size = 2
+indent_style = space
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[*.md]
+trim_trailing_whitespace = false

.env.example

@@ -0,0 +1,33 @@
+# ---------------------------------------------------------------------------- #
+
+# The name of the environment
+# prod  : prod
+# dev   : dev
+# local : local
+ENV_NAME='local'
+
+# ---------------------------------------------------------------------------- #
+
+# The path to the GTDB API
+# prod  : https://api.gtdb.ecogenomic.org
+# dev   : https://api.gtdb-dev.ecogenomic.org
+# local : http://0.0.0.0:9000
+API_BASE=http://0.0.0.0:9000
+
+# ---------------------------------------------------------------------------- #
+
+# The public reCaptcha site key
+# prod  :
+# dev   :
+# local :
+CAPTCHA_KEY=
+
+# ---------------------------------------------------------------------------- #
+
+# The google analytics tracking ID.
+# prod  :
+# dev   :
+# local :
+GA_TRACKING_ID=
+
+# ---------------------------------------------------------------------------- #

.eslintrc.js

@@ -0,0 +1,15 @@
+module.exports = {
+  root: true,
+  env: {
+    browser: true,
+    node: true
+  },
+  extends: [
+    '@nuxtjs/eslint-config-typescript',
+    'plugin:nuxt/recommended'
+  ],
+  plugins: [
+  ],
+  // add your custom rules here
+  rules: {}
+}

.github/workflows/main-push.yml

@@ -0,0 +1,21 @@
+name: Release
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  release:
+    name: release
+    runs-on: ubuntu-latest
+    steps:
+      # Semantic release
+      - uses: actions/checkout@v2
+      - uses: actions/setup-node@v2
+        with:
+          cache: npm
+          node-version: 16
+      - run: npm install --only=dev
+      - run: npx semantic-release
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -0,0 +1,97 @@
+# Created by .ignore support plugin (hsz.mobi)
+### Node template
+# Logs
+/logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# Directory for instrumented libs generated by jscoverage/JSCover
+lib-cov
+
+# Coverage directory used by tools like istanbul
+coverage
+
+# nyc test coverage
+.nyc_output
+
+# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# Bower dependency directory (https://bower.io/)
+bower_components
+
+# node-waf configuration
+.lock-wscript
+
+# Compiled binary addons (https://nodejs.org/api/addons.html)
+build/Release
+
+# Dependency directories
+node_modules/
+jspm_packages/
+
+# TypeScript v1 declaration files
+typings/
+
+# Optional npm cache directory
+.npm
+
+# Optional eslint cache
+.eslintcache
+
+# Optional REPL history
+.node_repl_history
+
+# Output of 'npm pack'
+*.tgz
+
+# Yarn Integrity file
+.yarn-integrity
+
+# dotenv environment variables file
+.env
+
+# parcel-bundler cache (https://parceljs.org/)
+.cache
+
+# next.js build output
+.next
+
+# nuxt.js build output
+.nuxt
+
+# Nuxt generate
+dist
+
+# vuepress build output
+.vuepress/dist
+
+# Serverless directories
+.serverless
+
+# IDE / Editor
+.idea
+
+# Service worker
+sw.*
+
+# macOS
+.DS_Store
+
+# Vim swap files
+*.swp
+
+# Manifest of files to store
+.dist-manifest
+
+# Public directory where files are served from
+public
+public_backup

.releaserc

@@ -0,0 +1,30 @@
+{
+  "tagFormat": "v${version}",
+  "branches": [
+    "main"
+  ],
+  "plugins": [
+    "@semantic-release/commit-analyzer",
+    "@semantic-release/release-notes-generator",
+    "@semantic-release/npm",
+    [
+      "@semantic-release/changelog",
+      {
+        "changelogFile": "CHANGELOG.md"
+      }
+    ],
+  [
+      "@semantic-release/git",
+      {
+        "assets": [
+          "CHANGELOG.md",
+          "package.json"
+        ],
+        "message": "chore(release): ${nextRelease.version} [skip ci]\n\n${nextRelease.notes}"
+      }
+    ],
+    [
+      "@semantic-release/github"
+    ]
+  ]
+}

README.md

@@ -1,2 +1,33 @@
 # gtdb.ecogenomic.org
-https://gtdb.ecogenomic.org/
+
+This repository hosts the GTDB website, the website uses [Vue](https://vuejs.org/guide/quick-start.html), based on
+the [Nuxt](https://nuxtjs.org/docs/get-started/installation) framework,
+using [TypeScript](https://www.typescriptlang.org/docs/handbook/intro.html).
+
+When the website is deployed, it is statically generated using `nuxt generate`, although this can be run locally with
+hot-reload for developing.
+
+## Contributing
+
+This project uses [Semantic Versioning](http://semver.org/) and [Conventional Commits](https://conventionalcommits.org/)
+to automatically generate release notes using [Semantic Release](https://semantic-release.gitbook.io/semantic-release/).
+
+Please ensure that your commits are property formatted.
+
+## Getting started
+
+```bash
+# install dependencies
+npm install
+
+# serve with hot reload at localhost:3000
+npm run dev
+
+# build for production and launch server
+npm run build
+npm run start
+```
+
+## Troubleshooting
+
+If you are getting (this as any) errors (or property doesn't exist on this). Then you have untyped computed properties.

assets/api/advanced.ts

@@ -0,0 +1,72 @@
+import axios from "axios";
+import {Dict} from "~/assets/ts/interfaces";
+
+const apiBase = process.env.apiBase;
+const apiTimeout = parseInt(process.env.apiTimeout || '30000');
+
+
+// --------------------------------------------------------------------------------------------
+// VIEW
+// --------------------------------------------------------------------------------------------
+
+export class AdvancedApi {
+
+  getOptions() {
+    return axios.get<AdvancedSearchOptionsResponse[]>(`${apiBase}/advanced/options`, {timeout: apiTimeout})
+  }
+
+  getOperators() {
+    return axios.get<AdvancedSearchOperatorResponse[]>(`${apiBase}/advanced/operators`, {timeout: apiTimeout})
+  }
+
+  getColumns() {
+    return axios.get<AdvancedSearchColumnResponse[]>(`${apiBase}/advanced/columns`, {timeout: apiTimeout})
+  }
+
+  getSearch(payload: Dict<string>) {
+    return axios.get<AdvancedSearchResult>(`${apiBase}/advanced/search`, {params: payload})
+  }
+
+  getSearchDownloadUrl(payload: Dict<string>) {
+    return axios.get<AdvancedSearchResult>(`${apiBase}/advanced/search`, {params: payload})
+  }
+
+}
+
+// --------------------------------------------------------------------------------------------
+// MODEL
+// --------------------------------------------------------------------------------------------
+
+export interface AdvancedSearchOptionsResponse {
+  id: number
+  display: string
+}
+
+export interface AdvancedSearchDataTypeResponse {
+  name: string
+  value: string
+}
+
+export interface AdvancedSearchOperatorResponse {
+  id: number
+  display: string
+  dataType: string
+}
+
+export interface AdvancedSearchColumnResponse {
+  id: number
+  display: string
+  dataType: string
+  options?: AdvancedSearchOptionsResponse[]
+  group: string
+}
+
+export interface AdvancedSearchHeader {
+  text: string
+  value: string
+}
+
+export interface AdvancedSearchResult {
+  headers: AdvancedSearchHeader[]
+  rows: Dict<any>[]
+}

assets/api/api.ts

@@ -0,0 +1,48 @@
+import axios, {AxiosError} from "axios"
+import {FastApiValidationError} from "~/assets/api/models";
+import {TaxonomyApi} from "~/assets/api/taxonomy";
+import {FastAniApi} from "~/assets/api/fastani";
+import {SpeciesApi} from "~/assets/api/species";
+import {GenomeApi} from "~/assets/api/genome";
+import {SankeyApi} from "~/assets/api/sankey";
+import {SearchApi} from "~/assets/api/search";
+import {TaxonApi} from "~/assets/api/taxon";
+import {AdvancedApi} from "~/assets/api/advanced";
+import {UtilApi} from "~/assets/api/util";
+
+export class API {
+  fastani = new FastAniApi();
+  genome = new GenomeApi();
+  sankey = new SankeyApi();
+  search = new SearchApi();
+  species = new SpeciesApi();
+  taxon = new TaxonApi();
+  taxonomy = new TaxonomyApi();
+  advanced = new AdvancedApi();
+  util = new UtilApi();
+}
+
+export function getApiErrorMessage(error: Error | AxiosError): string[] {
+  if (axios.isAxiosError(error)) {
+    if (error.response && error.response.data && error.response.data.detail) {
+
+      // Validation error
+      if (error.response.status === 422) {
+        const out = [];
+        const msg: FastApiValidationError[] = error.response.data.detail;
+        for (let i = 0; i < msg.length; i++) {
+          const curMsg = msg[i];
+          out.push(`${curMsg.loc[curMsg.loc.length - 1]}: ${curMsg.msg}`)
+        }
+        return out;
+      }
+
+      return [error.response.data.detail];
+
+    } else {
+      return [error.message];
+    }
+  } else {
+    return [error.message];
+  }
+}