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) )

familyAnnotations = annotations
  .filter(virus => virus.family == virusFamily)

function virusInfo(_family, _virus) {
  const info = 
    familyAnnotations.filter(row => row.abbreviation == _virus && row.family == _family)
  return info[0]
}

// Handle grouped viruses by extending the model with isGroup: false/true
addGrouped = (virus) => {
  const isGroup = (typeof virus.group_abbreviation !== "undefined") && (virus.group_abbreviation !== "")
  const virus_pointer = (isGroup) ? virus.group_abbreviation : virus.abbreviation 
  return (
    { ... virus,
      isGroup: isGroup,
      virusPointer: virus_pointer,
      resVirusId: (isGroup) ? virus.group_abbreviation : virus.abbreviation,
      resAbbreviation: (isGroup) ? virus.group_abbreviation : virus.abbreviation,
      resVirusName: (isGroup) ? virus.group_virus_name : virus.virus_name 
    }
  )
}

// Create a list of all viruses of interest in the Excel file
// Add group information early on
annotatedViruses =
  familyAnnotations
    .filter(virus => virus.virus_of_interest == "Yes")
    .map(virus => addGrouped(virus))

// Create a sublist of viruses with toolbox
// Take into account groups by selecting unique entries
toolboxAnnotatedViruses =
  annotatedViruses
    .filter(virus => virus.availability_in_toolbox == "Yes")
    .filter((value, index, self) => {
      return self.findIndex(v => v.resAbbreviation === value.resAbbreviation) === index;
    })

// Derive a virus object from the ID
// The ID can be either a virus_id (from the ictv tree) or a group_abbreviation
virusIdToVirus = (virus_id) => {

  // lookup the virus_id in the full list of viruses
  const fullList =
    annotatedViruses
      .filter(v => v.virus_id.replace(/^'+|'+$/g, '') == virus_id || v.abbreviation == virus_id)
      //.filter(v => v.virus_id == virus_id || v.abbreviation == virus_id)

  // lookup the abbreviation for the group
  const groupList =
    toolboxAnnotatedViruses
      .filter(v => v.group_abbreviation == virus_id)

  if (fullList.length > 0) {
    return fullList[0]
  }
  if (groupList.length > 0) {
    return groupList[0]
  }
}

// Return all matches for a virus ID
virusIdToViruses = (virus_id) => {
  // lookup the virus_id in the full list of viruses
  const single_virus =
    annotatedViruses
      .filter(v => v.virus_id.replace(/^'+|'+$/g, '') == virus_id || v.abbreviation == virus_id)
      [0]

  if (single_virus.isGroup) {
    return annotatedViruses
      .filter(v => v.group_abbreviation == single_virus.group_abbreviation)
  } else {
    return [ single_virus ]
  }
}

function renderVirusToolbox(family, virus_id) {

  // First extract the virus object from the ID or abbreviation
  // This takes into account the groups
  const virus = virusIdToVirus(virus_id)

  if (typeof virus.tools !== "undefined" && virus.tools.length > 0) {
    return html`
      ${toolbox.filter(tool => virus.tools.includes(tool.id) ).map(tool => 
        html`
        <h2 id="${tool.id}-section">${tool.name}</h2>
        <div class="container grid">
          <div class="g-col-12 g-col-md-3 toolbox one-tool" style="text-align:center;">
            <div id="toolbox-contents" class="tool-container">
              <a href="/toolbox/index.html#${tool.id}-section">
                <div class="tool-wrapper">
                  <div id="${tool.id}" class="tool">
                    <div class="tool-tooltip-text">${tool.name}</div>
                    ${tool.icon.map( i =>
                    html`<img class="tool-icon" height="${(tool.icon.length > 1) ? 150/tool.icon.length : 100}%" src="${i}"/>`
                    )}
                  </div>
                </div>
              </a>
            </div>
          </div>
          <div class="g-col-12 g-col-md-9">
            <p>${tool.description}</p>
          </div>
          <div class="g-col-1" style="text-align:center;">
          </div>
        </div>
        <div class="col-xs-12" style="height:20px;"></div>
        `
      )}
    `
  }
   else {
    return html`
      <p>&nbsp;</p>
    `
   }
}

import { virusInfoOrUndefinedF } from "/_js/functions.js"
import { availableVirusInfoF } from "/_js/functions.js"
import { availableToolsF } from "/_js/functions.js"
import { virusOfInterestF } from "/_js/functions.js"

// Initialize a container to contain the containers for the tree and annotation window
html`

<!-- Show information on hovered virus, reuse the same class for convenience -->
<div class="phylo-container">
  <!-- Left part -->
  <div class="left">
    <div id="info-container" class="text-center" style="visibility:hidden;">
        <div id="name" class="g-col-md-12 bold">
          name
        </div>
        <div id="toolbox" class="g-col-md-12">
          no tools yet for this virus
        </div>
    </div>
  </div>
  <!-- Right part -->
  <div id="annotation-container" class="right no-gutter">
    <p>&nbsp;</p>
  </div>
</div>

<div class="phylo-container">

  <!-- Left part -->
  <div class="left">
    <div id="tree-container" class="tree-container">
      <svg id="tree-svg" class="tree-svg"></svg>
    </div>
    <div id="legend-container" class="text-center mb-2">
      <div class="grid">
        <div class="g-col-md-12 small">
          <span class="phylotree-node-text" style="font-size:15px !important;">HOVER</span> for more information /
          <span class="phylotree-node-text-hl" style="font-size:15px !important;">BOLD NODES</span> are present in collection and can be selected 
        </div>
      </div>
    </div>
  </div>

  <!-- Right part -->
  <div id="annotation-container" class="right no-gutter">
    <div class="container grid small" align="center" style="--bs-gap: 1.0rem;font-weight:500;">
      <div class="g-col-md-12 g-col-sm-12 card card-body tool-header opacity-100" id="virus">
        Viral Toolbox
      </div>
    </div>
    <div class="container">
      <div class="toolbox">
          <div id="toolbox-contents" class="tool-container">
          </div>
      </div>
    </div>
  </div>

</div>
`

phylotree = await require("phylotree@1.1/dist/phylotree.js");

virusInfoOrUndefined = virusInfoOrUndefinedF(familyAnnotations)
availableVirusInfo = availableVirusInfoF(familyAnnotations)
availableTools = availableToolsF(familyAnnotations, toolbox)
virusOfInterest = virusOfInterestF(familyAnnotations)

// Initialize the toolbox when the data is loaded
init_toolbox =
  toolbox.map(tool =>
    d3.select("#toolbox-contents").node().append(
      html`
        <a href=${get_link("toolbox", "#" + tool.id + "-section")} target="_top">
          <div class="tool-wrapper">
            <div id="${tool.id}" class="tool">
              <div class="tool-tooltip-text">${tool.name}</div>
              ${tool.icon.map( i =>
              html`<img class="tool-icon" height="${(tool.icon.length > 1) ? 150/tool.icon.length : 100}%" src="${i}"/>`
              )}
            </div>
          </div>
        </a>
      `
    )
  )

// Reset the tools in the Toolbox
clearToolbox = () => {

  d3.select("#virus").text("Viral Toolbox")

  toolbox.map(tool => {
    d3.select("#" + tool.id).attr("class", "tool")
  })
}

// Update the tools in the toolbox based on the provided virus object
updateToolbox = (virus) => {

  d3.select("#virus").text(virus.resVirusName)
  toolbox
    .filter(tool => virus.tools.includes(tool.id))
    .map(tool =>
      d3.select("#" + tool.id).attr("class", "tool tool-selected")
    )
}

// Handle tabset depending on the number of tabs
rawTabs = d3.select("#vb-tabset").select("ul").selectAll("li").select("a").nodes()
nrTabs = rawTabs.length

function indexToTab(i, length) {
  const pre = "tabset-" + (length + 1) + "-"
  const post = "-tab"
  return pre + (i+1) + post
}
 
tabsetAnchor = indexToTab(0, nrTabs)

virusIdToTabMap = new Map(
  toolboxAnnotatedViruses
    .map( (virus,i) => [ virus.resAbbreviation, indexToTab(i, nrTabs) ] )
)

tabToVirusIdMap = new Map(
  Array.from(virusIdToTabMap, a => a.reverse())
)

// Hide virus information tabset
function hideTabset() {
  const virusInfo = document.getElementById(tabsetAnchor).parentNode.parentNode.parentNode
  virusInfo.style.display = "none"
}

hide = hideTabset()

// Instantiate tree
nwk = nwksAsMap[virusFamily]
tree = new phylotree.phylotree(nwk)   // class Phylotree
                                      // https://github.com/veg/phylotree.js/blob/master/src/main.js#L90

// import { update_tree } from "/_js/functions.js"

renderedTree = tree
  // Transform the tree (translate and prune)
  // based on the input Excel file for this virus family
  .traverse_and_compute(node => {

    const virus_id = node.data.name
    const isLeaf = tree.isLeafNode(node)

    if (isLeaf) {
      const virus = virusIdToVirus(virus_id)
      const isVirusOfInterest = (typeof virus !== "undefined") ? (virus.virus_of_interest == "Yes") : false
      if (isVirusOfInterest) {
        const currentName = virus_id
        const newName = virus.abbreviation.trim()
        node.data.name = newName
      } else {
        node.data.name = "remove_me"
        tree.deleteANode(node)
      }
    } 
  })
  .render({
    'width': 600,
    'height': 600,
    'left-right-spacing':  'fit-to-size',
    'top-bottom-spacing':  'fit-to-size',
    'is-radial':          true,
    'selectable':         false,
    'collapsible':        false,
    'transitions' :       false,
    'show-menu':          false,
    'show-scale':         false,
    'align-tips':         true,
    'zoom':               false,
    'brush':              false,
    'draw-size-bubbles':  false,
    'maximum-per-node-spacing': 500,
    'minimum-per-node-spacing': 100,
    'maximum-per-level-spacing': 500,
    'minimum-per-level-spacing': 100,
    'container': "#tree-container"
  })
  .style_nodes( (element, data) => {
    // the virus_id is how the virus is encoded in phylotree newick file
    const virus_id = data.data.name  
    
    // At this stage in the process, every node should have information
    const information = virusIdToVirus(virus_id) // virusInfoOrUndefined(virus_id)

    const inToolbox = (typeof information !== "undefined") && (information.availability_in_toolbox == "Yes")

    // Styling based on available information
    const updtElement1 =
      information 
        ? element.select("text").attr("class", "phylotree-node-text")
        : element.select("text").attr("class", "phylotree-node-text-inactive")
    const updtElement = inToolbox ? element.select("text").attr("class", "phylotree-node-text-hl") : element

    // Hover functionality - Virus name
    if (information)
      element
        .on("mouseover", virusHoverIn(data, information, inToolbox))
        .on("mouseout", virusHoverOut)
 
    // Click functionality - Toolbox
    inToolbox
      ? element.on('click', function(el) {
          clearToolbox();
          // Select the first tab in order to get to the root of the tabset
          const virusInfo = document.getElementById(tabsetAnchor).parentNode.parentNode.parentNode
          virusInfo.style.display = "block"
          virusInfo.scrollIntoView(true)
          // Now get the proper tab and open it
          const thisVirusInfo = document.getElementById(virusIdToTabMap.get(information.virusPointer))  // either the virus_id or the group abbreviation
          thisVirusInfo.click();

          // Experiments
          clearNodes()
          highlightNodes(virus_id)

          // Render the toolbox for this virus
          updateToolbox(information);
        })
      : element.on('click', function() {
          hideTabset()
          clearToolbox()
        })

  })
  .layout(true)

// Based on a virus ID (abbreviation), highlight the virus or the whole group it belongs to
highlightNodes = (virus_id) => {
  const abbreviations = virusIdToViruses(virus_id).map(v => v.abbreviation)

  d3.selectAll("g")
    .filter(function (d) { return (typeof d.data !== "undefined") ? abbreviations.includes(d.data.name) : false})
    .select("text").attr("class", "phylotree-node-text-selected")

}

// Initialize all viruses in the tree
clearNodes = () => {
  const inLst = annotatedViruses.map(v => v.abbreviation)
  const inToolboxLst = annotatedViruses.filter(v => v.availability_in_toolbox == "Yes").map(v => v.abbreviation)

  // Initialize all text
  d3.selectAll("g")
    .filter(function (d) { return (typeof d.data !== "undefined") })
    .select("text").attr("class", "phylotree-node-text")

  // Update toolbox entries
  d3.selectAll("g")
    .filter(function (d) { return (typeof d.data !== "undefined") ? inToolboxLst.includes(d.data.name) : false})
    .select("text").attr("class", "phylotree-node-text-hl")
}

// console.log(renderedTree)

showTree = renderedTree
  .svg
  .node()

// Show small virus information box on hover
virusHoverIn = (data, information, is_available) => () => {
  // First, populate the content
  const virusNameToShow =
    (information.resVirusName)
      ? information.resVirusName
      : (typeof information.virus_name !== "undefined")
        ? information.virus_name
        : ""
  d3.select("#name").text(virusNameToShow)
  if (information.tools.length > 0)
    d3.select("#toolbox").text("Viral tools are available, please select the virus for more information")
  else
     d3.select("#toolbox").text("No viral tools have been developed yet")
  // ... then show the content
  d3.select("#info-container").attr("style", "visibility:visible;")
}

virusHoverOut = () => {
  d3.select("#info-container").attr("style", "visibility:hidden;")
}

// Clicking on the tabs feeds the info back to the toolbox info
feedbackToolbox = d3.selectAll(".nav-item")
  .on('click', function(){
    const _id = d3.select(this).select("a").attr('id')
    const _virus_id = tabToVirusIdMap.get(_id)
    // We should only update the toolbox if an actual virus is selected
    // not if for instance the 'toolbox' tab is selected
    if (typeof _virus_id !== "undefined") {
      const _virus = virusIdToVirus(_virus_id)
      clearToolbox();
      updateToolbox(_virus)
      clearNodes()
      highlightNodes(_virus_id)
    }
  })
     
// Add SVG to the DOM
tmp = d3.select("#tree-container").node().appendChild(showTree)

// If the size of the SVG is smaller than the allocated 600px
// then resize it relatively to the fraction
// Allow for a bit of padding, hence the .95 factor.
newSizeF = (curSize) => {
    if (curSize < 600) {
      return 600 * (0.95 * 600 / curSize)
    } else {
        return curSize
    }
  }

newSize = newSizeF(renderedTree.size[0])
updateSize = renderedTree.set_size([newSize,newSize]).update()

 

MARV

Symptoms

Transmission

Medical relevance

The first case of the Marburgvirus disease was reported in 1967 when lab personnel working with African green monkeys got infected in Germany and Serbia simultaneously.

Following the initial case, many more outbreaks occurred around the world such as Uganda, Sudan, South Africa, Angola, Congo, Kenya and even in the United States in 2008

Toolbox

The toolbox for this virus is currently in development. Please contact us via info@virusbankplatform.be for more information.

renderVirusToolbox("filoviruses", "MARV")

open virus page / reload family page

EBOV

Symptoms

Transmission

Medical relevance

Originally named for Zaire (now the Democratic Republic of the Congo), the country where the virus was first described.

Disease incidence mainly restricted to Africa. More specifically DRC, South Africa, Gabon, Guniea and republic of Congo and Uganda.

Toolbox

The toolbox for this virus is currently in development. Please contact us via info@virusbankplatform.be for more information.

renderVirusToolbox("filoviruses", "EBOV")

open virus page / reload family page