package miniScripts;

import java.io.IOException;
import java.io.StringReader;
import java.net.URL;
import java.net.URLConnection;
import java.util.Scanner;


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.InputSource;
import org.xml.sax.SAXException;

public class queryVariant {

	public static void main (String [] arg) throws IOException {

		String gene = "BRAF";
		String term = "V600E";
		String urltxt = "http://goldorak.hesge.ch/synvar/generate/litterature/fromMutation";
		String param = "?base="+gene+"&variant="+term+"&type=protein";
			
		String content = "";
		try{
			URL url = new URL(urltxt+param);
			URLConnection connection = url.openConnection();
			connection.connect();
			Scanner in = new Scanner(connection.getInputStream());
			while(in.hasNextLine()){
				String line = in.nextLine();
				content += line+"\n"; 
			}
			in.close();
		} catch (Exception e){
			System.out.println("error downloading:"+e.toString());
		}
		

		// Transform the content to an XML object
		try {
			DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
			DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
			InputSource is = new InputSource(new StringReader(content));
			Document doc = dBuilder.parse(is);
			doc.getDocumentElement().normalize();
			
			// Get the variant list
			NodeList variantList = doc.getElementsByTagName("variant");	
			// Pour chaque variant
			for (int v = 0; v < variantList.getLength(); v++) {
				
				Node variantNode = variantList.item(v);
				Element variantElement = (Element) variantNode;
								
				// Get data at protein level
				Node proteinNode = variantElement.getElementsByTagName("protein-level").item(0);
				if (proteinNode != null) {
				Element proteinElement = (Element) proteinNode;
				
					// Get HGVS
					NodeList hgvsPList = proteinElement.getElementsByTagName("hgvs");
					if (hgvsPList.getLength() != 0){
						Node hgvsPNode = hgvsPList.item(0);
						String hgvsP = hgvsPNode.getTextContent().trim();
						System.out.println(hgvsP);

					}

					// Get synonyms
					NodeList synoProteinNode = proteinElement.getElementsByTagName("syntactic-variation");
					for (int s=0; s<synoProteinNode.getLength(); s++) {
						Node synoNode = synoProteinNode.item(s);
						String synonym = synoNode.getTextContent().trim();
						System.out.println(synonym);

					}
				}
					
				// Get data at transcript level
				Node transcriptNode = variantElement.getElementsByTagName("transcript-level").item(0);
				if (transcriptNode != null) {
				Element transcriptElement = (Element) transcriptNode;
				
					// Get HGVS
					NodeList hgvsTList = transcriptElement.getElementsByTagName("hgvs");
					if (hgvsTList.getLength() != 0){
						Node hgvsTNode = hgvsTList.item(0);
						String hgvsT = hgvsTNode.getTextContent().trim();
						System.out.println(hgvsT);


					}
				
					// Get synonyms
					NodeList synoTranscriptNode = transcriptElement.getElementsByTagName("syntactic-variation");
					for (int s=0; s<synoTranscriptNode.getLength(); s++) {
						Node synoNode = synoTranscriptNode.item(s);
						String synonym = synoNode.getTextContent().trim();
						System.out.println(synonym);

					}
				}
			
				// Get data at genome level
				Node genomeNode = variantElement.getElementsByTagName("genome-level").item(0);
				if (genomeNode != null) {
				Element genomeElement = (Element) genomeNode;
				
					// Get HGVS
					NodeList hgvsGList = genomeElement.getElementsByTagName("hgvs");
					if (hgvsGList.getLength() != 0){
						Node hgvsGNode = hgvsGList.item(0);
						String hgvsG = hgvsGNode.getTextContent().trim();
						System.out.println(hgvsG);

					}
				
					// Get synonyms
					NodeList synoGenomeNode = genomeElement.getElementsByTagName("syntactic-variation");
					for (int s=0; s<synoGenomeNode.getLength(); s++) {
						Node synoNode = synoGenomeNode.item(s);
						String synonym = synoNode.getTextContent().trim();
						System.out.println(synonym);
					}
				}
				
				
			}
			
						
		} catch (ParserConfigurationException | SAXException | IOException e) {
			//e.printStackTrace();
			System.out.println("Variant "+term+" failed to be normalized by goldorak");
		}

		
		
		
	}
	
	
}