EDIT

package org.cybertaxonomy.utis.refine;

import java.io.IOException;

import java.io.InputStream;

import java.io.StringWriter;

import java.net.URI;

import java.net.URISyntaxException;

import java.util.ArrayList;

import java.util.Iterator;

import java.util.List;

import org.apache.commons.io.IOUtils;

import org.apache.http.Header;

import org.apache.http.HttpEntity;

import org.apache.http.client.methods.CloseableHttpResponse;

import org.apache.http.client.methods.HttpPost;

import org.apache.http.client.utils.URIBuilder;

import org.apache.http.entity.ByteArrayEntity;

import org.apache.http.entity.mime.MultipartEntityBuilder;

import org.apache.http.impl.client.CloseableHttpClient;

import org.apache.http.impl.client.HttpClients;

import org.apache.http.message.BasicHeader;

import org.apache.http.util.EntityUtils;

import org.cybertaxonomy.utis.checklist.DRFChecklistException;

import org.cybertaxonomy.utis.utils.JSONUtils;

import org.json.simple.JSONObject;

public class RefineClient {

	private static String boundary = "----dcBoundary";

	private String server;

	private String port;

	public RefineClient(String server, String port) {

		this.server = server;

		this.port=port;

	}

	public String initJob() throws IOException, DRFChecklistException, URISyntaxException {

		String jobID = null;

		List<Header> headers = new ArrayList<Header>();

		headers.add(new BasicHeader("Content-Type","application/http"));

		headers.add(new BasicHeader("Accept","application/json"));

		URIBuilder uriBuilder = getURIBuilder(server,port,"/command/core/create-importing-job");

		String initResponse = callCoreRefineService(uriBuilder.build(),headers,null);

		JSONObject jsonResponse = (JSONObject) JSONUtils.parseJsonToObject(initResponse);

		Long jobIDLong = (Long)jsonResponse.get("jobID");

		if(jobIDLong != null) {

			jobID = String.valueOf(jobIDLong);

		}

		return jobID;

	}

	public String uploadData(String csvData, String jobID) throws RefineException, IOException, URISyntaxException {

		String uploadResponse = "";

		if(csvData != null && !csvData.isEmpty()) {

			MultipartEntityBuilder meBuilder = getMEBuilder();

			meBuilder.setBoundary(boundary);

			String lineEnding = "\r\n";	

			String beginStr = "--" + boundary + lineEnding +

					"Content-Disposition: form-data; name=\"upload\"; filename=\"dcinput.txt\"" + lineEnding +

					"Content-Type: text/plain" + lineEnding + lineEnding;

			String endStr = lineEnding + "--" + boundary + "--";

			//String inputBody = beginStr + csvData.replaceAll(System.getProperty("line.separator"),"\r\n") + endStr;

			String inputBody = beginStr + csvData + endStr;

			meBuilder.addBinaryBody("input", inputBody.getBytes());

			List<Header> headers = new ArrayList<Header>();

			headers.add(new BasicHeader("Content-Type","multipart/form-data; boundary=" + boundary));

			headers.add(new BasicHeader("Accept","text/html"));

			URIBuilder uriBuilder = getURIBuilder(server,port,"/command/core/importing-controller");

			uriBuilder.setParameter("jobID", jobID);

			uriBuilder.setParameter("subCommand","load-raw-data");

			uriBuilder.setParameter("controller","core/default-importing-controller");

			uploadResponse = callCoreRefineService(uriBuilder.build(),headers,new ByteArrayEntity(inputBody.getBytes()));

		} else {

			throw new RefineException("Data to be uploaded to Refine server is null or empty");

		}

		return uploadResponse;

	}

	public boolean checkImportJobStatus(String jobID) throws IOException, URISyntaxException, DRFChecklistException {

		boolean importDone = false;

		String checkResponse;

		List<Header> headers = new ArrayList<Header>();

		headers.add(new BasicHeader("Content-Type","multipart/form-data"));

		headers.add(new BasicHeader("Accept","application/json"));

		URIBuilder uriBuilder = getURIBuilder(server,port,"/command/core/get-importing-job-status");

		uriBuilder.setParameter("jobID", jobID);

		while(!importDone) {

			checkResponse = callCoreRefineService(uriBuilder.build(),headers,null);

			System.out.println("importJobCheck : " + checkResponse);

			JSONObject jsonResponse = (JSONObject) JSONUtils.parseJsonToObject(checkResponse);

			JSONObject job = (JSONObject)jsonResponse.get("job");

			JSONObject config = (JSONObject)job.get("config");

			boolean hasData = (Boolean)config.get("hasData");

			String state = (String)config.get("state");

			if(hasData && state.equals("ready"))

				importDone = true;

		}

		return importDone;

	}

	public String initializeParser(String jobID) throws IOException, URISyntaxException {

		List<Header> headers = new ArrayList<Header>();

		headers.add(new BasicHeader("Content-Type","application/xml"));

		headers.add(new BasicHeader("Accept","application/json"));

		URIBuilder uriBuilder = getURIBuilder(server,port,"/command/core/importing-controller");		

		uriBuilder.setParameter("controller","core/default-importing-controller");

		uriBuilder.setParameter("jobID", jobID);

		uriBuilder.setParameter("subCommand","initialize-parser-ui");

		uriBuilder.setParameter("format","text/line-based/*sv");

		return  callCoreRefineService(uriBuilder.build(),headers,null);				

	}

	public String updateFormat(String jobID) throws IOException, URISyntaxException {

		List<Header> headers = new ArrayList<Header>();

		headers.add(new BasicHeader("Content-Type","application/x-www-form-urlencoded"));

		headers.add(new BasicHeader("Accept","application/json"));

		String options = "options={\"encoding\":\"\",\"separator\":\",\",\"ignoreLines\":-1,\"headerLines\":1,\"skipDataLines\":0,\"limit\":-1,\"storeBlankRows\":false,\"guessCellValueTypes\":true,\"processQuotes\":true,\"storeBlankCellsAsNulls\":true,\"includeFileSources\":false,\"projectName\":\"" + jobID + "\"}";

		URIBuilder uriBuilder = getURIBuilder(server,port,"/command/core/importing-controller");		

		uriBuilder.setParameter("controller","core/default-importing-controller");

		uriBuilder.setParameter("jobID", jobID);

		uriBuilder.setParameter("subCommand","update-format-and-options");

		uriBuilder.setParameter("format","text/line-based/*sv");				

		return  callCoreRefineService(uriBuilder.build(),headers,new ByteArrayEntity(options.getBytes()));				

	}

	public String createProject(String jobID) throws IOException, URISyntaxException {

		List<Header> headers = new ArrayList<Header>();

		headers.add(new BasicHeader("Content-Type","application/x-www-form-urlencoded"));

		headers.add(new BasicHeader("Accept","application/json"));

		String options = "options={\"encoding\":\"\",\"separator\":\",\",\"ignoreLines\":-1,\"headerLines\":1,\"skipDataLines\":0,\"limit\":-1,\"storeBlankRows\":false,\"guessCellValueTypes\":true,\"processQuotes\":true,\"storeBlankCellsAsNulls\":true,\"includeFileSources\":false,\"projectName\":\"" + jobID + "\"}";

		URIBuilder uriBuilder = getURIBuilder(server,port,"/command/core/importing-controller");		

		uriBuilder.setParameter("controller","core/default-importing-controller");

		uriBuilder.setParameter("jobID", jobID);

		uriBuilder.setParameter("subCommand","create-project");		

		uriBuilder.setParameter("format","text/line-based/*sv");

		return  callCoreRefineService(uriBuilder.build(),headers,new ByteArrayEntity(options.getBytes()));				

	}

	public String checkCreateProjectStatus(String jobID) throws IOException, URISyntaxException, DRFChecklistException, InterruptedException {

		boolean createDone = false;

		String checkResponse;

		List<Header> headers = new ArrayList<Header>();

		headers.add(new BasicHeader("Content-Type","application/xml"));

		headers.add(new BasicHeader("Accept","application/json"));

		URIBuilder uriBuilder = getURIBuilder(server,port,"/command/core/get-importing-job-status");

		uriBuilder.setParameter("jobID", jobID);

		Long percent;

		String projectID = null;

		while(!createDone) {

			checkResponse = callCoreRefineService(uriBuilder.build(),headers,null);

			System.out.println("createProjectCheck : " + checkResponse);

			JSONObject jsonResponse = (JSONObject) JSONUtils.parseJsonToObject(checkResponse);

		    JSONObject job = (JSONObject)jsonResponse.get("job");

		    JSONObject config = (JSONObject)job.get("config");

		    JSONObject progress = (JSONObject)config.get("progress");

		    if(progress != null) {

		    	percent = (Long)progress.get("percent");

		    	Long projectIDLong = (Long)config.get("projectID");

		    	projectID = String.valueOf(projectIDLong);

		    	createDone = (percent == 100);

		    }

		    Thread.sleep(1000);

		}

		return projectID;

	}

	public String deleteProject(String projectID) throws IOException, URISyntaxException {

		List<Header> headers = new ArrayList<Header>();

		headers.add(new BasicHeader("Content-Type","application/x-www-form-urlencoded"));

		headers.add(new BasicHeader("Accept","application/json"));		

		URIBuilder uriBuilder = getURIBuilder(server,port,"/command/core/delete-project");		

		uriBuilder.setParameter("project", projectID);

		return  callCoreRefineService(uriBuilder.build(),headers,null);		

	}

	public String exportData(String projectID) throws RefineException, IOException, URISyntaxException {

		List<Header> headers = new ArrayList<Header>();

		headers.add(new BasicHeader("Content-Type","application/x-www-form-urlencoded"));

		headers.add(new BasicHeader("Accept","text/html"));		

		URIBuilder uriBuilder = getURIBuilder(server,port,"/command/core/export-rows/" + projectID + ".csv");		

		uriBuilder.setParameter("project", projectID);

		uriBuilder.setParameter("engine","{\"facets\":[],\"mode\":\"row-based\"}");		

		uriBuilder.setParameter("format","csv");

		return  callCoreRefineService(uriBuilder.build(),headers,null);		

	}

	public String callCoreRefineService(URI uri,

			List<Header> headers,

			HttpEntity reqEntity) throws IOException {

		String responseString = null;

		CloseableHttpClient httpClient = HttpClients.createDefault();

		try {

			HttpPost httpPost = new HttpPost(uri);

			Iterator<Header> headerItr = headers.iterator();

			while(headerItr.hasNext()) {

				httpPost.addHeader(headerItr.next());

			}

			if(reqEntity != null) {				

				httpPost.setEntity(reqEntity);						

			}

			System.out.println("executing request " + httpPost.getRequestLine());

			CloseableHttpResponse response = httpClient.execute(httpPost);

			try {

				System.out.println("----------------------------------------");

				System.out.println(response.getStatusLine());

				System.out.println(response.toString());

				HttpEntity resEntity = response.getEntity();

				if (resEntity != null) {

					StringWriter writer = new StringWriter();

					responseString = contentToString(resEntity.getContent());

					System.out.println(responseString);

					System.out.println("Response content length: " + resEntity.getContentLength());

				}

				EntityUtils.consume(resEntity);

			} finally {

				response.close();

			}

		} finally {

			httpClient.close();

		}

		return responseString;

	}

	public MultipartEntityBuilder getMEBuilder() {		

		MultipartEntityBuilder meBuilder = MultipartEntityBuilder.create();

		return meBuilder;

	}

	private String contentToString(InputStream content) throws IOException {

		StringWriter writer = new StringWriter();

		IOUtils.copy(content, writer, "UTF-8");

		return writer.toString();

	}

	private URIBuilder getURIBuilder(String host, String port, String path) {

		URIBuilder uriBuilder = new URIBuilder();		

		uriBuilder.setScheme("http");

		uriBuilder.setHost(host);

		uriBuilder.setPort(Integer.valueOf(port));

		uriBuilder.setPath(path);

		return uriBuilder;

	}

}