Develop

.github/workflows/quarto_gh_pages.yml

@@ -8,7 +8,7 @@ on:
       - synchronize
       - closed
 
-name: Render and deploy to Netlify
+name: Render and deploy to Netlify and VirusBank
 
 jobs:
   build-deploy:
@@ -24,12 +24,16 @@ jobs:
       - name: Assemble alpha/toolbox.json 
         uses: mikefarah/yq@master
         with:
-          cmd: yq -M -o=json '. *d load("alpha/src/toolbox.yaml")' _includes/toolbox.yaml > alpha/toolbox.json
+          cmd: yq -M -o=json src/toolbox.yaml > toolbox/toolbox.json
 
-      - name: Assemble alpha/annotations.json
-        uses: mikefarah/yq@master
+      - uses: r-lib/actions/setup-r@v2
         with:
-          cmd: yq -M -o=json alpha/src/annotations.yaml > alpha/annotations.json
+          r-version: "4.2"
+          use-public-rspm: true
+
+      - name: Install rmarkdown
+        run: |
+          Rscript -e 'install.packages("rmarkdown")'
 
       - name: Install Quarto
         uses: quarto-dev/quarto-actions/setup@v2
@@ -60,7 +64,19 @@ jobs:
           site: ${{ env.NETLIFY_SITE_ID }}
           dir: '_site'
           alias: "${{ env.BRANCH_NAME }}"
-          message: 'Deploy prooduction ${{ github.ref }}'
+          message: 'Deploy production ${{ github.ref }}'
+
+      # - name: Deploy preview to VirusBank
+      #   id: deploy_virusbank
+      #   if: github.event_name == 'pull_request'
+      #   uses: SamKirkland/[email protected]
+      #   with:
+      #     server: ftp.virusbankplatformorg.webhosting.be
+      #     username: floor@virusbankplatformorg
+      #     password: ${{ secrets.FTP_AUTH_SECRET }}
+      #     local-dir: './_site/'
+      #     log-level: standard
+          # dangerous-clean-slate: true
 
       - uses: thollander/actions-comment-pull-request@v2
         if: github.event_name == 'pull_request'

README.md

@@ -0,0 +1,35 @@
+# VirusBank Phylotree project
+
+## Requirements and setup
+
+In order to *render* this site/app, the following are required:
+
+0.  `wget`
+
+1.  Quarto
+
+2.  `yq`:
+
+    ``` sh
+    sudo wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64
+    sudo chmod a+x /usr/local/bin/yq
+    ```
+
+## Rendering
+
+## Setup
+
+### Toolbox page
+
+The toolbox page is based on a YAML file.
+
+### Virus family pages
+
+Every virus family is contained in a *folder* of its own. Inside this
+folder, everything related to this specific family can be found.
+
+### Virus pages
+
+## Various remarks
+
+- `d3` is loaded by Quarto already, there is not need to load it again

README.qmd

@@ -0,0 +1,41 @@
+---
+title: VirusBank Phylotree project
+format: gfm
+---
+
+## Requirements and setup
+
+In order to _render_ this site/app, the following are required:
+
+0. `wget`
+
+1. Quarto
+
+2. `yq`:
+
+    ```sh
+    sudo wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64
+    sudo chmod a+x /usr/local/bin/yq
+    ```
+
+## Rendering
+
+## Setup
+
+### Toolbox page
+
+The toolbox page is based on a YAML file.
+
+### Virus family pages
+
+Every virus family is contained in a _folder_ of its own. Inside this folder, everything related to this specific family can be found.
+
+### Virus pages
+
+
+
+## Various remarks
+
+- `d3` is loaded by Quarto already, there is not need to load it again
+
+

_js/_ojs_data.qmd

@@ -0,0 +1,63 @@
+```{ojs}
+//| echo: false
+//| output: false
+
+// Utility functions
+import { encodeTool } from '/_js/functions.js'
+
+FA = FileAttachment
+
+// Load the toolbox
+families = await FA("/families.json").json()
+_toolbox = await FileAttachment("/toolbox/toolbox.json").json()
+toolbox = _toolbox.map( tool => encodeTool(tool) )
+
+// console.log(toolbox)
+
+addEncodedTools = (virus) => {
+  return ({ ... virus, tools: toolbox.flatMap( tool => virus[tool.encoded] ? tool.id : []) }) 
+}
+
+// Load all Newick tree file and create a dictionary `family -> tree`
+nwks = await Promise.all(
+  families.map(async (family) => { 
+    let tree = await FA("/"+ family + "/tree.newick").text()
+    return ({ family: family, nwk: tree })
+  }))
+nwksAsMap = Object.fromEntries(nwks.map( el => [el.family, el.nwk] ))
+
+// console.log(nwks)
+
+// Load annotations for viruses for each family
+_annotations = await Promise.all(
+  families.map( async (family) => {
+    let xls = await FA("/"+ family + "/family.xlsx").xlsx()
+    let _annotations = xls.sheet(0, { headers: true, range: ":L" })
+
+    let _trimmed = _annotations.map( virus => {
+      let trimmed = {}
+      Object.keys(virus).forEach( key => {
+        trimmed[key] = virus[key].trim()
+      })
+      return trimmed
+    })
+
+    return _trimmed.map( virus => ({... virus, family: family }) )
+  }))
+
+// console.log(_annotations)
+
+// Add tools information, just the list of tools ids
+annotations = _annotations
+  .flat()
+  .map( virus => addEncodedTools(virus) )
+
+//console.log(
+//  annotations
+//    .filter(v => v.availability_in_toolbox == "Yes")
+//    .filter(v => v.tools.length == 0)
+//    .map(v => "Family: " + v.family + " / virus: " + v.abbreviation)
+//    .join("\n")
+//)
+
+```