Purdue Entomology's TaxonPages

Purdue Entomological Research Collection (PERC) homepage: https://ag.purdue.edu/department/entm/perc/

The PERC instance of TaxonPages has four repos, each with its own GitHub Pages site — because a repo can only have a single GitHub Pages site. They diverge only in their base_url in the file config/router.yml.

Repo	Destination	`base_url` in `router.yml`
taxonpages	Github Pages: https://purdueentomologicalresearchcollection.github.io/taxonpages/	`/taxonpages/`
taxonpages-deploy	Cascade — see action log for deployment: https://ag.purdue.edu/department/entm/perc/search-collection.html	`/department/entm/perc/search-collection.html`
taxonpages-dev	Github Pages: https://purdueentomologicalresearchcollection.github.io/taxonpages-dev/	`/taxonpages-dev/`
taxonpages-deploy-dev	Cascade — see action log for deployment: https://ag.purdue.edu/department/agit/test/perc/	`/department/agit/test/perc/`

Each uses GitHub Actions, following these instructions. Deployment is automatic for those hosted on Github Pages, but for Cascade it requires manual steps of copying files. For now. In the future, hopefully we can automate Cascade deployments using the Cascade API.

TODO: Explain how to deploy to Cascade

Local Development

You'll need to clone multiple repos into a single local git repo. This may be a new experience — even for seasoned developers — but it works very well because it's a core feature of git.

Clone the production repo, like you would normally. This will become your origin remote.

git clone git@github.com:PurdueEntomologicalResearchCollection/taxonpages.git
cd taxonpages

Add the dev repo as a remote and configure dev branches.

git remote add dev git@github.com:PurdueEntomologicalResearchCollection/taxonpages-dev.git
git fetch dev
git checkout -b dev-setup dev/setup
git checkout -b dev-main dev/main

Run the dev-main branch locally. You can follow the usual dev cycle — make changes , edit code, commit, repeat.

git checkout dev-main
git checkout dev-setup .  # Yes, this is a funky thing to do, and you will have to clean up before committing
npm install
npm run dev

Open http://localhost:5173/taxonpages-dev/ to try it out, see changes hot reload, etc.

Commit and push changes. This push will seem a little weird, if you haven't worked with multiple repos before.

git commit -m "a good description of this commit"
git push dev HEAD:main  # push to repository taxonpages-dev's the main branch

This will trigger a rebuild in Github Pages, and after a minute or so, the deployed version will be ready to test at https://purdueentomologicalresearchcollection.github.io/taxonpages-dev/

Congratulations, you have made changes locally and published them to Github Pages!

Deploying Changes to Cascade CMS

After you make changes locally, you'll want to push them up the chain to the Purdue test page and then to the production PERC search page.

Tidy up your local branch. Be sure you have committed your changes before you do this, because this step will erase anything that is not committed.
- The branch deploy-dev is the taxonpages-deploy-dev repository's main branch, if you followed the setup steps above.
- Again, this will trigger a rebuild, but in the deploy-dev repo, but that version will not work because it is configured to run inside Cascade CMS.

git reset --hard  # Warning: This will totally wipe out any changes you haven't committed.

If you haven't already, add two more git remotes:

git checkout -b deploy-setup deploy/setup
git checkout -b deploy-main deploy/main
git checkout -b deploy-dev-setup deploy-dev/setup
git checkout -b deploy-dev-main deploy-dev/main

Deploy to Cascade CMS testing page.
- First, merge to deploy-dev. Github Actions will build a new version, that you can deploy.

git checkout deploy-dev
git merge dev  # follow prompts to pull your new changes into the deploy-dev branch

Download the zip file of artifacts by clicking on the latest Github Actions workflow run → build → Upload artifact → Artifact download URL
Upload the assets from that zip file to Cascade CMS, in the appropriate assets folder. It should be 4 files — one .css and three .js.
In Cascade CMS, edit the HTML to refer to the new files. You will need to edit two filenames: one .css and one .js.
Publish your changes. After 10-15 minutes, it will be live on the PERC Search Test Page.

Promote to production, once testing is complete.
- Merge to the main and/or deploy branches, similar to above.
- See your changes in Github Pages: https://purdueentomologicalresearchcollection.github.io/taxonpages/
- Deploy to the main PERC search page.
- Voila, site updated!

Upstream changes

To keep up with upstream changes — and also to contribute back — you'll need to connect with the Species File Group's github repo: https://github.com/SpeciesFileGroup/taxonpages.

Catching up with upstream development

Add the remotes (this may be familiar by now)

git remote add sfg https://github.com/SpeciesFileGroup/taxonpages.git
git checkout -b sfg-main sfg/main
git checkout -b sfg-setup sfg/setup

Merge upstream changes to your dev branch.

git checkout dev-main
git merge sfg-main  # there will likely be conflicts, homework, npm install, testing, etc — plan for this to take a while
git checkout dev-setup
git merge sfg-setup  # probably straightforward? Let's hope.

Test and merge these changes into your other branches, and follow the steps as above for deployment.

Contributing upstream

The pinnacle of open source development: Contributing back to the community!

This is an advanced topic, and you will need to be in touch with the Species File Group (SFG) developers. The Purdue Entomology faculty and staff can help you get connected. You will create a pull request and review it with SFG developers.

TaxonPages

TaxonPages is a tool to serve taxon pages. At present it draws data from TaxonWorks' API, however we seek to keep the TaxonPages platform agnostic therefor facilitating the modular addition of functionality that may reference data from any biodiversity data-serving API.

Status Warning

TaxonPages software is in active development and changes are expected that will cause the early first-adopters' instances to require rebuilding by refreshing one's forked branch using git pull. A first stable version is expected by Spring 2023.

Usage

Click on "Fork" button to create your own repository from this.
Uncheck Copy the setup branch only and press Save
After create your repo, go to Settings > Pages, on "Build and deployment - Source" select GitHub Actions.
Go to Actions tab and press I understand my workflows, go ahead and enable them button
Open router.yml file and change base_url to the name of your repository.
After a couple of minutes, your public page should be available at https://<your_user_name>.github.io/<your_repo_name>

Setup

Switch to setup branch in your TaxonPages repository.
We provide some settings by default to setup your public pages, but API parameters are required and must be configured to get the data from your TaxonWorks project.

# config/api.yml
---
url: https://<your.taxonworks.server>/api/v1
project_token: yourprojecttoken

Push the changes after update the configuration files inside setup branch
GitHub actions will build TaxonPages with the current configuration in setup branch and publish it to the gh-pages branch

Install

Follow this steps to run TaxonPages in your local machine.

Install NodeJS
We recommend you to fork this repository to keep getting updates. Use GIT to clone the repo.

git clone https://github.com/<your_username>/<your_repository_name>.git

But if you don't want to fork it, you can clone directly from this

git clone https://github.com/SpeciesFileGroup/taxonpages.git

Go to taxonpages folder and enter the following commands to copy the software to your setup branch

git checkout main
git checkout setup
git checkout main .
git reset
git checkout .

Setup config/api.yml with the API server configuration
Install node dependencies

npm install

Start TaxonPages

npm run dev

TaxonPages will be running at http://localhost:5173/

Customization

Pages

TaxonPages out of the box support markdown and vue for content sites. Add your content pages inside pages folder. By default, TaxonPages use the file name to create the route. For example, if the filename is "contributors.md" the route to access it will be http://yourtaxonpagessite/contributors

Markdown pages

This software use vite-plugin-md to render pages in Markdown format, the engine of this plugin is markdown-it. For plugins and other configuration you can refer to this section https://github.com/antfu/vite-plugin-md#configuration--options

Example: welcome.md file

---
name: 'Charles Darwin'
---

# Welcome, {{ name }}!

To use TaxonPage internal variables in config/*.yml, you can either do so by adding the prefix {{ app:var_name }} or use the script tag in your markdown page and get them from the global object __APP_ENV__

Prefix

# Welcome to {{ app:project_name }}!

Script tag

# Welcome to {{ project_name }}!

<script setup>
const { project_name } = __APP_ENV__
</script>

Components

TaxonPages global components are enable in your markdown pages, by default we provide a set of global components that you don't need to import them to use it. You can see the list of this global components here

Style

If you want to change the color palette, you can edit /config/style/theme.css file, colors must be in RGB format. TaxonPages use TailwindCSS framework for the style. We already provide default settings for colors and markdown. If you want to make any change to your configuration, you must do so in the config/vendor/tailwind.config.js file. This file uses the TaxonPages configuration as a default. It is possible to overwrite it as long as you use it as a preset.

Analytics

TaxonPages has out-of-the-box support for the following list of analytics services:

analytics_services:
  enableDev: false # Set true to work in development mode
  analytics:   # Google Analytics
    - id: 'G-XXXXX'
  gtm:         # Google Tag Manager
    - id: 'GTM-XXXXX'
  pixel:       # Facebook Pixel
    - id: 'XXXXXXX'
  retargeting: # VK Retargeting
    - id: 'VK-RTRG-XXXXXX-XXXXX',
  linkedin:    # Linkedin Insight
    - id: 'XXXXXXX'
  tongji:      # Baidu Tongji
    - id: 'XXXXXXX',
  metrica:     # Yendex Metrica
    - id: 'XXXXXXX',
  microsoft:   # Microsoft Analytics
    id: 'XXXXXXX'
  hotjar:      # Hotjar Analytics
    id: 'XXXXXXX',
  fullStory:   # Full story Analytics
    org: 'X-XXXXXX-XXX'
  tiktok:      # TikTok Pixel Analytics
    id: 'XXXXXXX'

Deep dive into TaxonPages

Access internal configuration vars

To access the configuration in *.yml files, we provide a global object that contains all the configuration values. This variable can be used in either JavaScript, Vue, or Markdown files. To access these values you must use the __APP_ENV__ variable:

const { project_name } = __APP_ENV__
// or
const projectName = __APP_ENV__.project_name

Taxa Page

Layout

To modify the position of the panels in the layout of the Taxa page, edit the taxa_page.yml file. There you can add/move/remove panels from the layout, also you can add new tabs and include new panels there. If you want to make some tabs visible or not depending the rank group, you can include rankGroup

taxa_page:
  overview:
    panels:
      - - - panel:gallery
          - panel:type
          - panel:type-specimen
          - panel:nomenclature
          - panel:nomenclature-references

        - - panel:map
          - panel:descendants
          - panel:content
          - panel:statistics
#
# An example of a new tab:
#
# type_specimens:
#   rank_group: ['SpeciesGroup']
#   panels:
#     - - - panel:specimen-records

Lifecycle hooks (Experimental feature)

The onCreatePage and onSSRPageCreate functions allow you to execute code at the time the taxa page is created. onSSRPageCreate will be executed only on the server side in SSR mode. To make use of them it is necessary to include them in a file object called pages/otus.config.js. Both functions accept otu, taxon, route and router objects as parameters. Since onCreatePage runs on Taxa page component, it is possible to use hooks like onMounted or onBeforeMount inside it

export default {
  onSSRCreatePage: async ({ otu, taxon, route, router }) => {
    // Your code here
  },

  onCreatePage: ({ otu, taxon, route, router }) => {
    // Your code here
  }
}

Customizing the Layout

The application comes with a default layout that includes a header and a footer. If you'd like to replace this layout with your own, you can do so by creating a custom layout file.

Steps to replace the default layout

In the root folder of your project, create a new folder called layouts (if it doesn't already exist).
Inside this folder, create a file named default.vue.
Define your custom layout structure inside this file as needed.

Example of layouts/default.vue

<template>
  <div>
    <slot />
  </div>
</template>

This custom layout will replace the default one and be applied throughout the application. You can include your own elements, such as a navigation bar or footer, as needed.

Using Multiple Layouts

In addition to replacing the default layout, you can create multiple layouts by adding more .vue files inside the layout folder. You can then specify which layout to use for a specific page by setting the layout name in the meta property of the <route> tag in your Single File Component (SFC).

JSON5:

<route>
{
  meta: {
    layout: 'custom'
  }
}
</route>

YAML:

<route lang="yaml">
meta:
  layout: custom
</route>

External panels

To add panels in Taxa pages, create a folder called panels in your setup branch, and inside it create another folder for your panel. For example: panels/PanelTest

In PanelTest folder, create a main.js file, with the following structure:

import MyPanelComponent from './MyPanelComponent.vue'

Export default {
   id: 'panel:test', // ID to identify this panel
   component: MyPanelComponent, // Vue component for your panel
   rankGroup: ['HigherClassificationGroup', 'FamilyGroup', 'GenusGroup', 'SpeciesGroup'] // <-- OPTIONAL: This will define for which rank group will be available, remove it if your panel will be available for all.
}

This file is used to load your panel component in taxa page. Use the id to include and define the position in the layout in taxa_page.yml

taxa_page_overview:
  panels:
    - - - panel:gallery
        - panel:test # <--- Your new panel
        - panel:type
        - panel:type-specimen
        - panel:nomenclature
        - panel:nomenclature-references

      - - panel:map
        - panel:descendants
        - panel:content
        - panel:statistics

Defining global components

TaxonPages provides an auto-import component from src/components and /components folders using special extensions for it. Some objects and functions are only present in the browser and not in the NodeJs server environment. When you run code that is not supported by the server, it ends up crashing. Some JavaScript libraries like Leaflet use the document or window object, which do not exist in the node environment. To handle this problem, TaxonPages provides 2 ways to import the components.

Client Side only (CSR):

This auto import method will only load the component on the client side, while on the server it will create a fake empty component, which will be used later on the client side to be replaced by the original one when the hydration process occurs. To define this type of import, the component name must contain the word .client. before .vue extension.

Example: MyAmazingComponent.client.vue

Global (CSR & SSR)

This auto-import method will load the component both client and server side. To define this type of import, the component must contain the word .client. before the .vue extension.

Example: MyAmazingComponent.global.vue

Global components

TaxonPages provides a set of global components that could be used to create your own panels or pages. Here is the complete list:

Component	Description	Props
`<AnimationOpacity/>`	Add an opacity animation for a child component
`<Autocomplete/>`	Used to perform searches in TaxonWorks	Link
`<AutocompleteOtu/>`	A specific autocomplete for OTU search
`<ClientOnly/>`	Render child components only from client side
`<VButton/>`	Button component
`<VCard/>`	Card component style
`<VCardContent/>`	Card content body
`<VCardHeader/>`	Card Header
`<VClipboard/>`	Copy a text to clipboard
`<Dropdown/>`	Dropdown menu
`<GalleryImage/>`		Link
`<ImageViewer/>`
`<TrackerReport/>`	Show trackers to report issues	Link
`<TabMenu/>`
`<TabItem/>`
`<VMap/>`	Interactive map that use Leaflet library
`<VModal/>`	Create lightboxes
`<VSkeleton/>`	Content loading placeholder
`<VSpinner/>`	Loading spinner
`<VTable/>`
`<VTableBody/>`
`<VTableBodyCell/>`
`<VTableBodyRow/>`
`<VTableHeader/>`
`<VTableHeaderCell/>`
`<VTableHeaderRow/>`

Icons
`<IconArrowDown/>`
`<IconArrowLeft/>`
`<IconArrowRight/>`
`<IconCheck/>`
`<IconClipboard/>`
`<IconClose/>`
`<IconDocument/>`
`<IconDownload/>`
`<IconHamburger/>`
`<IconJson/>`
`<IconMinusCircle/>`
`<IconPlusCircle/>`
`<IconSearch/>`
`<IconTrash/>`
`<IconWarning/>`

wbbaker/taxonpages

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