package project_Task1;

import java.io.BufferedReader;
import java.io.DataOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.ProtocolException;

import java.net.URL;
import java.io.InputStream;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;

import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.SAXException;

import java.util.HashMap;
import java.util.Map;
import java.util.Scanner;  // Import the Scanner class

public class API_Call {

    public static void main (String args[]) throws IOException, ParserConfigurationException, SAXException{

        URL url = null;
        URL url_citing_article = null;
        String url_string = "";
        String url_string_articles_citations = "";
        String url_string_citing_article = "";

        Scanner myObj = new Scanner(System.in);  // Create a Scanner object
        System.out.println("Please enter DOI:");

        String doi = myObj.nextLine();  // Read user input
        if (doi.contentEquals("")) {
            doi = "10.7554/eLife.15550";
            System.out.println("No DOI entered. Using example DOI: " + doi);
        }else {
            System.out.println("DOI is:" + doi);
        }

        // DOI to PMID ID Converter (API DOCS: https://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/)
        String url_convert_string = "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?"
                + "tool=citation_network&email=brad.w.english@gmail.com&ids="
                + doi;

        url = new URL(url_convert_string);


        DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
        DocumentBuilder docBuilder = dbf.newDocumentBuilder();

        URL url1 = new URL(url_convert_string);
        InputStream stream = url1.openStream();
        Document doc = docBuilder.parse(stream);

        NodeList record_list = doc.getElementsByTagName("record");
        String pmid_string = "";
        for(int i=0;i<record_list.getLength();i++) {
            Node record_node = record_list.item(i);
            Element record = (Element) record_node;
            pmid_string = record.getAttribute("pmid");
            System.out.println("The PMID is " + pmid_string);
        }


        // (API DOCS: https://www.ncbi.nlm.nih.gov/pmc/tools/cites-citedby/)

        System.out.print("\nPMIDs of cited articles:\n");
        url_string_articles_citations = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?"
                + "dbfrom=pubmed&linkname=pubmed_pubmed_refs&id="
                + pmid_string;

        url = new URL(url_string_articles_citations);

        DocumentBuilderFactory dbf_citations = DocumentBuilderFactory.newInstance();
        DocumentBuilder docBuilder_citations = dbf_citations.newDocumentBuilder();

        InputStream stream_citations = url.openStream();
        Document doc_citations = docBuilder_citations.parse(stream_citations);

        NodeList link_list = doc_citations.getElementsByTagName("Id");
        for(int i=0;i<link_list.getLength();i++) {
            Node citation_node = link_list.item(i);
            Element citation = (Element) citation_node;
            System.out.print(citation.getTextContent() +',');
        }

        System.out.print("\nPMIDs which cite this article:\n");
        url_string_citing_article = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?"
                + "dbfrom=pubmed&linkname=pubmed_pubmed_citedin&id="
                + pmid_string;

        url_citing_article = new URL(url_string_citing_article);

        DocumentBuilderFactory dbf_citing_article = DocumentBuilderFactory.newInstance();
        DocumentBuilder docBuilder_citing_article = dbf_citing_article.newDocumentBuilder();

        InputStream stream_citing_article = url_citing_article.openStream();
        Document doc_citing_article = docBuilder_citing_article.parse(stream_citing_article);

        NodeList citing_article_link_list = doc_citing_article.getElementsByTagName("Id");
        for(int i=0;i<citing_article_link_list.getLength();i++) {
            Node citing_article_node = citing_article_link_list.item(i);
            Element citing_article = (Element) citing_article_node;
            System.out.print(citing_article.getTextContent() + ',');
        }





    }
}