@plantinformatics/vcf-genotype-brapi/src/utils/data/ipk-panbarlex-browser.js

Client and server functions to access genotype data from VCF via a custom web API and BrAPI

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/** Base of web API endpoint URLs of IPK PanBARLEX
 */
const baseUrl = 'https://panbarlex.ipk-gatersleben.de';

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/**
 * Represents an interval selected ("brushed") on a chromosome axis by the user.
 * @typedef {object} Interval
 * @property {string} genotype - The genotype to fetch data for.
 * @property {string} contig - The contig to fetch data for.
 * @property {number} start - The starting position of the data range.
 * @property {number} end - The ending position of the data range.
 */

/**
 * Fetches dot plot data from the web API.
 *
 * Explanation :
 * This function accepts parameters for `genotype`, `contig`, `start`, and `end`, allowing you to fetch different data sets based on user input or other dynamic values.
 * It constructs the request body based on these parameters and performs the fetch operation.
 * It checks if the response is OK and then parses the JSON data if it is.
 *
 * Error Handling :
 * The function includes error handling to log any issues with the fetch operation.
 *
 * The first version of this function was partially generated by ChatGPT based
 * on /dotplot network request recorded by Web Inspector `Copy as Fetch`.
 *
 * @param {Interval[]} intervals - An array of objects each containing the parameters
 *  - {genotype, contig, start, end}
 *
 * @returns {Promise<Object>} The JSON response from the API containing the dot plot data.
 * @throws {Error} Will throw an error if the fetch operation fails or the response is not OK.
 */
export async function fetchDotPlotData(intervals) {
  const
  fnName = 'fetchDotPlotData',
  url = baseUrl + '/assemblies/dotplot',
  entries = intervals.slice(0, 2)
    .map((interval, i) => [["1st", "2nd"][i] , interval]),
  params = Object.fromEntries(entries),
  body = JSON.stringify(params);
  try {
    const response = await fetch(url, {
      method: "POST", // Method is required
      body: body,     // Request body
      mode: "cors"    // CORS mode
    });

    if (!response.ok) {
      throw new Error(`HTTP error! status: ${response.status}`);
    }

    const data = await response.json();
    return data;

  } catch (error) {
    console.error("Error fetching dot plot data:", error);
    throw error; // Rethrow so the caller can handle it
  }
}

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// test data for Dotplot Types :
const
Self_Alignment =
  [
    {
      genotype: "Akashinriki",
      contig: "chr1H",
      start: 0,
      end: 200
    }],
Pairwise_Alignment =
  [
    {
      contig : "chr1H",
      end : 100,
      genotype : "RGT_Planet",
      start : 0,
    },
    {
      contig : "chr1H",
      end : 100,
      genotype : "OUN333",
      start : 0,
    }];

/**
 * Example function to retrieve dot plot data and log it to the console.
 * This demonstrates how to call `fetchDotPlotData` with sample parameters and handle the result.
 *
 * Usage : // Call the example function
 *  getDotPlot();
 */
async function getDotPlot() {
  try {
    const
    params = Self_Alignment,
    // params = Pairwise_Alignment,
    result = await fetchDotPlotData(params);
    console.log("Dot plot data:", result);
    // Process the result as needed
  } catch (error) {
    console.error("Failed to get dot plot data:", error);
  }
}


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