main.gs

String.prototype.capitalize = function () {
  return this.charAt(0).toUpperCase() + this.slice(1);
};

/**
 * @OnlyCurrentDoc
 *
 * The above comment directs Apps Script to limit the scope of file
 * access for this add-on. It specifies that this add-on will only
 * attempt to read or modify the files in which the add-on is used,
 * and not all of the user's files. The authorization request message
 * presented to users will reflect this limited scope.
 */

/**
 * Creates a menu entry in the Google Docs UI when the document is opened.
 * This method is only used by the regular add-on, and is never called by
 * the mobile add-on version.
 *
 * @param {object} e The event parameter for a simple onOpen trigger. To
 *     determine which authorization mode (ScriptApp.AuthMode) the trigger is
 *     running in, inspect e.authMode.
 */
function onOpen(e) {
  DocumentApp.getUi()
    .createMenu("Semantically")
    .addItem("Launch Semantically Workspace", "showSidebar")
    .addToUi();
  init();
}

/**
 * Runs when the add-on is installed.
 * This method is only used by the regular add-on, and is never called by
 * the mobile add-on version.
 *
 * @param {object} e The event parameter for a simple onInstall trigger. To
 *     determine which authorization mode (ScriptApp.AuthMode) the trigger is
 *     running in, inspect e.authMode. (In practice, onInstall triggers always
 *     run in AuthMode.FULL, but onOpen triggers may be AuthMode.LIMITED or
 *     AuthMode.NONE.)
 */
function onInstall(e) {
  onOpen(e);
}

function init() {
  if (
    PropertiesService.getScriptProperties().getProperty(
      "automaticHighlighting"
    ) == null
  ) {
    PropertiesService.getScriptProperties().setProperty(
      "automaticHighlighting",
      "false"
    );
  }
}

/**
 * Opens a sidebar in the document containing the add-on's user interface.
 * This method is only used by the regular add-on, and is never called by
 * the mobile add-on version.
 */
function showSidebar() {
  var ui =
    HtmlService.createHtmlOutputFromFile("sidebar").setTitle("Semantically");
  DocumentApp.getUi().showSidebar(ui);
}

function getAnnotations(enableHighlighting) {
  if (enableHighlighting === true) {
    PropertiesService.getScriptProperties().setProperty(
      "highlightingEnabled",
      true
    );
  }

  annotations = [];

  // Getting Annotations
  var url = "https://data.bioontology.org/annotator";
  var result = JSON.parse(
    UrlFetchApp.fetch(url, {
      muteHttpExceptions: true,
      method: "POST",
      payload: {
        text: DocumentApp.getActiveDocument().getBody().getText(),
        include: "prefLabel,definition",
        display_context: "false",
        apikey: "89f4c54e-aee8-4af5-95b6-dd7c608f057f",
      },
    })
  );

  for (i = 0; i < result.length; i++) {
    annotations.push({
      id: result[i]["annotatedClass"]["@id"],
      prefLabel: result[i]["annotatedClass"]["prefLabel"].capitalize(),
      definition:
        typeof result[i]["annotatedClass"]["definition"] !== "undefined"
          ? result[i]["annotatedClass"]["definition"][0]
              .split(/<p>|<\/p>/)
              .join("")
          : "",
      ontology: result[i]["annotatedClass"]["links"]["ontology"].replace(
        /http[s]?:\/\/data.bioontology.org\/ontologies\//g,
        ""
      ),
      link: result[i]["annotatedClass"]["links"]["self"],
      annotations: result[i]["annotations"],
    });
  }

  return JSON.stringify(annotations);
}

function getRecommenderAnnotations() {
  // Getting Recommender Annotations
  var url = "https://data.bioontology.org/recommender";
  var result = UrlFetchApp.fetch(url, {
    muteHttpExceptions: true,
    method: "POST",
    payload: {
      input: DocumentApp.getActiveDocument().getBody().getText(),
      display_context: "false",
      display_links: "false",
      apikey: "89f4c54e-aee8-4af5-95b6-dd7c608f057f",
    },
  }).getContentText();
  Logger.log(result);
  var ontologyId = /"ontologies":\[[\S ]*?"acronym":"([\S ]*?)"/g.exec(
    result
  )[1];
  recommenderAnnotations = JSON.parse(
    /"annotations":(\[[\S ]*?\])/g.exec(result)[1]
  );
  for (i = 0; i < recommenderAnnotations.length; i++) {
    recommenderAnnotations[i].ontology = ontologyId;
  }

  highlightAnnotations();

  return JSON.stringify(recommenderAnnotations);
}

function getCurrentPosition() {
  var offset = DocumentApp.getActiveDocument()
    .getBody()
    .editAsText()
    .getText()
    .indexOf(
      DocumentApp.getActiveDocument()
        .getCursor()
        .getElement()
        .asText()
        .getText()
    );
  var offsetPosition = DocumentApp.getActiveDocument()
    .getCursor()
    .getSurroundingTextOffset();
  return offset == 0 &&
    DocumentApp.getActiveDocument().getCursor().getElement().asText().getText()
      .length == 0
    ? -1
    : offset + offsetPosition;
}

function highlightAnnotations() {
  //Logger.log(annotations.length);
  if (
    PropertiesService.getScriptProperties().getProperty("highlightingEnabled")
  ) {
    Logger.log(recommenderAnnotations.length);
    var text = DocumentApp.getActiveDocument().getBody().editAsText();
    text.setBackgroundColor(0, text.getText().length - 1, null);
    for (i = 0; i < recommenderAnnotations.length; i++) {
      text.setBackgroundColor(
        recommenderAnnotations[i]["from"] - 1,
        recommenderAnnotations[i]["to"] - 1,
        "#FCFC00"
      );
    }
  }
}

function unhighlightAnnotations() {
  PropertiesService.getScriptProperties().setProperty(
    "highlightingEnabled",
    false
  );

  var text = DocumentApp.getActiveDocument().getBody().editAsText();
  text.setBackgroundColor(0, text.getText().length - 1, null);
}

function getHtml() {
  return DocumentApp.getActiveDocument().getBody().getText();
}