ImportSDD.java

package org.hadatac.console.controllers.dataacquisitionsearch;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.InputStream;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.io.IOException;

import play.*;
import play.mvc.*;
import play.mvc.Http.MultipartFormData;
import play.mvc.Http.MultipartFormData.FilePart;
import play.libs.*;

import org.apache.commons.csv.CSVRecord;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.hadatac.console.controllers.annotator.AnnotationLog;
import org.hadatac.console.views.html.dataacquisitionsearch.*;
import org.hadatac.data.loader.ccsv.Parser;
import org.hadatac.data.loader.util.Arguments;
import org.hadatac.data.loader.util.FileFactory;
import org.hadatac.entity.pojo.Credential;
import org.hadatac.metadata.loader.LabkeyDataHandler;
import org.hadatac.utils.ConfigProp;
import org.hadatac.utils.Feedback;
import org.kohsuke.args4j.Option;
import org.labkey.remoteapi.CommandException;

public class ImportSDD extends Controller {

	static FileFactory files;

	public static final String UPLOAD_NAME = "uploads/sdd.csv";
	
    public static Result importSDD(String oper) {
    	return ok(importSDD.render(oper, ""));
    }

//    public static Result postLoadSDD(String oper) {
//    	return ok(importSDD.render(oper, ""));
//    }
    
//    public Map<String, Object> createRow() {
//    	Map<String, Object> row = new HashMap<String, Object>();
//    	row.put("hasURI", getUri());
//    	row.put("a", getType());
//    	row.put("rdfs:label", getTitle());
//    	row.put("skos:definition", getAims());
//    	row.put("rdfs:comment", getSignificance());
//    	row.put("hasco:hasAgent", getAgent());
//    	row.put("hasco:hasInstitution", getInstitution());
//    	counter++;
//    	
//    	return row;
//    }
//    
//    public List< Map<String, Object> > createRows() {
//    	for (CSVRecord record : records) {
//    		rec = record;
//    		rows.add(createRow());
//    	}
//
//    	return rows;
//    }
    
    public static void playLoadSDD() throws IOException, CommandException {	

		BufferedReader reader = new BufferedReader(new FileReader(UPLOAD_NAME));
		List<List<String>> lines = new ArrayList<>();
		String line = null;
		while ((line = reader.readLine()) != null) {
			List<String> elephantList = Arrays.asList(line.split(","));
		    lines.add(elephantList);
		}
		
		Map<String, List<String>> sddMap = new HashMap<String, List<String>>();
		for (int i = 0; i < lines.size(); i++){
			sddMap.put("i", lines.get(i));
		}
//		System.out.println(lines.get(0).get(0));
		
		Map<String, Object> row = new HashMap<String, Object>();
		List< Map<String, Object> > rows = null;
		
		String site = ConfigProp.getPropertyValue("labkey.config", "site");
		String path = "/SIDPIDTEST";
        Credential cred = Credential.find();

    	LabkeyDataHandler labkeyDataHandler = new LabkeyDataHandler(
    			site, cred.getUserName(), cred.getPassword(), path);

		int nRows = labkeyDataHandler.updateRows("DASchemaAttribute", rows);
		
		reader.close();
   }
    
    @BodyParser.Of(value = BodyParser.MultipartFormData.class, maxLength = 500 * 1024 * 1024)
    public static Result uploadFile() {
    	MultipartFormData body = request().body().asMultipartFormData();
    	FilePart uploadedfile = body.getFile("sddsheet");
    	if (uploadedfile != null) {
    		File file = uploadedfile.getFile();
    		File newFile = new File(UPLOAD_NAME);
    		InputStream isFile;
    		try {
    			isFile = new FileInputStream(file);
    			byte[] byteFile;
    			try {
    				byteFile = IOUtils.toByteArray(isFile);
    				try {
    					FileUtils.writeByteArrayToFile(newFile, byteFile);
    				} catch (Exception e) {
    					e.printStackTrace();
    				}
    				try {
    					isFile.close();
    				} catch (Exception e) {
    					return ok (importSDD.render("fail", "Could not save uploaded file."));
    				}
    			} catch (Exception e) {
    				return ok (importSDD.render("fail", "Could not process uploaded file."));
    			}
    		} catch (FileNotFoundException e1) {
    			return ok (importSDD.render("fail", "Could not find uploaded file"));
    		}
    		return ok(importSDD.render("loaded", "File uploaded successfully."));
    	} else {
    		return ok (importSDD.render("fail", "Error uploading file. Please try again."));
    	}
    }
}