annotate common.js @ 0:b58b229c4cbf draft

planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty

this.ctx = () => context;
var all_contexts = [] ;
var inchidata = {} ;
var all_mix_data = {} ;
function no_success(tab_index, inchi, data) {
  console.log(`inchikey ${inchi} not found...`) ;
  console.log(`disabling ${data} ...`)
  disable_tab(
    tab_index,
    "red",
    "This compound has not been found on peakforest"
  ) ;
}

function disable_tab(tab_index, color, title) {
  var element = $(`#open_tab_${tab_index}`) ;
  element.attr("disabled", "disabled").off("click");
  element.attr("onclick", null) ;
  element.attr("title", title) ;
  element.attr("data-toggle", null) ;
  element.attr("href", null) ;
  element.css("color", color) ;
  element.css("cursor", "not-allowed") ;
}

function send_everything_to_peakforest(url, token) {
  var bundles ;
  if (context.is_mix()) {
    bundles = [all_mix_data] ;
  } else {
    bundles = create_dataset_bundles() ;
  }
  bundles.forEach((bundle, index) => {
    console.log(bundle)
    $.ajax({
      type: "post",
      url: `${url}/rest/v2/spectrum?token=${token}`,
      data: JSON.stringify(bundle),
      contentType: "application/json"
    })
  })
  // console.log(bundles)
}

function create_dataset_bundles() {
  var bundles = [] ;
  var data ;
  all_contexts.forEach((context, index) => {
    if ((data = context.sent_json) === null) {
      return ;
    }
    if (bundles.length === 0) {
      // console.log("First metadata!")
      return bundles.push(data) ;
    }
    if (merge_in_bundle(bundles, data)) {
      // console.log("Merged!")
    } else {
      // console.log("New metadata!")
    }
  }) ;
  return bundles ;
}

function merge_in_bundle(bundles, data) {
  for(var i = 0 ; i < bundles.length ; i += 1) {
    if (
      identical(bundles[i]["sample"], data["sample"])
      && identical(bundles[i]["chromatography"], data["chromatography"])
      && identical(bundles[i]["analyzer"], data["analyzer"])
      && identical(bundles[i]["ionization_mode_positive"], data["ionization_mode_positive"])
      && identical(bundles[i]["ionization_mode_negative"], data["ionization_mode_negative"])
      && identical(bundles[i]["other_metadata"], data["other_metadata"])
    ) {
      bundles[i]["peaklists"].push(data["peaklists"][0]) ;
      return true ;
    } else {
      continue ;
      console.log(
        "sample: "
        + identical(bundles[i]["sample"], data["sample"])
      )
      console.log(
        "chromatography: "
        + identical(bundles[i]["chromatography"], data["chromatography"])
      )
      console.log(
        "analyzer: "
        + identical(bundles[i]["analyzer"], data["analyzer"])
      )
      console.log(
        "ionization_mode_positive: "
        + identical(bundles[i]["ionization_mode_positive"], data["ionization_mode_positive"])
      )
      console.log(
        "ionization_mode_negative: "
        + identical(bundles[i]["ionization_mode_negative"], data["ionization_mode_negative"])
      )
      console.log(
        "other_metadata: "
        + identical(bundles[i]["other_metadata"], data["other_metadata"])
      )
    }
  }
  bundles.push(data) ;
  return false ;
}

function identical(left, right) {
  if (typeof left !== typeof right) {
    return false ;
  }
  if (left === null) {
    return right === null ;
  }
  if (right === null) {
    return left === null ;
  }
  switch (typeof left) {
    case "array":
      return identical_array(left, right) ;
      break ;
    case "object":
      return identical_object(left, right) ;
      break ;
    default:
      break ;
  }
  return (left === right)
}

function identical_array(left, right) {
  if (right.length !== left.length) {
    return false ;
  }
  for(var i = 0 ; i < left.length ; i += 1) {
    if (!identical(left[i], right[i])) {
      return false ;
    }
  }
  return true ;
}

function identical_object(left, right) {
  var left_keys ;

  if (!(
    share_keys(left, right)
    && share_keys(right, left)
  )) {
    return true ;
  }
  left_keys = Object.keys(left) ;
  for (var i = 0 ; i < left_keys.length ; i += 1){
    if (!identical(left[left_keys[i]], right[left_keys[i]])) {
      return false ;
    }
  }
  return true ;
}

function share_keys(left, right) {
  var left_keys ;
  var right_keys ;

  left_keys = Object.keys(left) ;
  right_keys = Object.keys(right) ;
  for(var i = 0 ; i < left_keys.length ; i += 1) {
    if (!right_keys.includes(left_keys[i])) {
      return false ;
    }
  }
  return true ;
}

var set_inchi_data = function(data, tab_index) {
  inchidata[data.inchikey] = data ;
  $(`#add1spectrum-sample-inchi-${tab_index}`).val(data.inchi);
  $(`#add1spectrum-sample-inchi-${tab_index}`).change();
  $(`#add1spectrum-sample-commonName-${tab_index}`).val(data.name);
  $(`#add1spectrum-sample-commonName-${tab_index}`).change();
  $(`#sample-bonus-display-${tab_index}`).html(
    `<img
      class=""
      src="{{ PF_URL_PLACEHOLDER }}/webapp/image/${data.type}/${data.inchikey}"
      alt="${data.name}"
    >`
  );
}

var lightgrayRenderer = function(instance, td, row, col, prop, value, cellProperties) {
  Handsontable.renderers.TextRenderer.apply(this, arguments);
  td.style.backgroundColor = "#EEE";
}