cirad.cgh.vcf2fasta.Vcf2fastaWebServiceCall.java Source code

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Here is the source code for cirad.cgh.vcf2fasta.Vcf2fastaWebServiceCall.java

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/*******************************************************************************
 * Copyright (C) 2016 <CIRAD>
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License, version 3 as
 * published by the Free Software Foundation.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 * See the GNU Affero General Public License for more details.
 *
 * See <http://www.gnu.org/licenses/gpl-3.0.html> for details about
 * GNU Affero General Public License V3.
 *
 * Contributors:
 *     Anestis Gkanogiannis <ganoyan@gmail.com>
 *******************************************************************************/
package cirad.cgh.vcf2fasta;

import cirad.cgh.vcf2fasta.beans.Vcf2fastaInputBean;
import cirad.cgh.vcf2fasta.ws.gatk_alternativefasta.AppServiceLocator;
import cirad.cgh.vcf2fasta.ws.gatk_alternativefasta.AppServicePortType;
import cirad.cgh.vcf2fasta.ws.gatk_alternativefasta.types.InputFileType;
import cirad.cgh.vcf2fasta.ws.gatk_alternativefasta.types.JobInputType;
import cirad.cgh.vcf2fasta.ws.gatk_alternativefasta.types.JobOutputType;
import cirad.cgh.vcf2fasta.ws.gatk_alternativefasta.types.JobSubOutputType;
import cirad.cgh.vcf2fasta.ws.gatk_alternativefasta.types.OutputFileType;

import java.io.Serializable;
import java.rmi.RemoteException;

import javax.xml.rpc.ServiceException;

import org.apache.commons.configuration.XMLConfiguration;

public class Vcf2fastaWebServiceCall implements Serializable {

    private static final long serialVersionUID = 3526225275691004383L;

    private XMLConfiguration config;

    public Vcf2fastaWebServiceCall(XMLConfiguration config) {
        this.config = config;
    }

    @SuppressWarnings("unused")
    public IVcf2fastaWebServiceCall makeVcf2fastaCall(Vcf2fastaInputBean vcf2fastaInputBean) throws Exception {
        String program = vcf2fastaInputBean.getAccession();

        IVcf2fastaWebServiceCall vcf2fastaCall = null;
        String jobID = null;
        vcf2fastaCall = new Vcf2fastaCall(config);
        jobID = vcf2fastaCall.makeVcf2fastaCall(vcf2fastaInputBean);

        return vcf2fastaCall;
    }

}

interface IVcf2fastaWebServiceCall {
    public int getStatusCode();

    public String makeVcf2fastaCall(Vcf2fastaInputBean vcf2fastaInputBean);

    public String getResultURL();
}

class Vcf2fastaCall implements IVcf2fastaWebServiceCall {

    private XMLConfiguration config;

    private AppServicePortType servicePort;
    private String jobID = null;

    public Vcf2fastaCall(XMLConfiguration config) {
        this.config = config;
    }

    public synchronized AppServicePortType getService() {
        if (servicePort == null) {
            try {
                servicePort = new AppServiceLocator().getAppServicePort();
            } catch (ServiceException e) {
                e.printStackTrace();
            }
        }
        return servicePort;
    }

    public synchronized int getStatusCode() {
        if (jobID == null) {
            return -1;
        }
        try {
            if (servicePort == null) {
                servicePort = getService();
            }
            return servicePort.queryStatus(jobID).getCode();
        } catch (Exception e) {
            return -1;
        }
    }

    public synchronized String getResultURL() {
        if (servicePort == null) {
            servicePort = getService();
        }

        OutputFileType outFile = null;
        JobOutputType outputs = null;
        try {
            outputs = servicePort.getOutputs(jobID);
        } catch (RemoteException e) {
            e.printStackTrace();
            return null;
        }

        for (OutputFileType tmp : outputs.getOutputFile()) {
            if (tmp.getUrl().toString().endsWith("out.fasta"))
                outFile = tmp;
        }

        if (outFile != null) {
            return outFile.getUrl().toString();
        } else {
            return null;
        }
    }

    //Returns jobID
    @SuppressWarnings("unused")
    public synchronized String makeVcf2fastaCall(Vcf2fastaInputBean vcf2fastaInputBean) {
        if (servicePort == null) {
            servicePort = getService();
        }

        String accession = vcf2fastaInputBean.getAccession();
        String contig = vcf2fastaInputBean.getContig();
        String interval = vcf2fastaInputBean.getInterval();

        String vcf_prefix = config
                .getString("analyses/analysis[@name='" + vcf2fastaInputBean.getAnalysis() + "']/vcf_prefix");
        String vcf_suffix = config
                .getString("analyses/analysis[@name='" + vcf2fastaInputBean.getAnalysis() + "']/vcf_suffix");

        StringBuilder arguments = new StringBuilder();
        arguments.append(" --variant " + vcf_prefix + "/" + accession + vcf_suffix);
        if (contig != null && contig != "") {
            arguments.append(" --intervals " + contig + ":" + interval);
        }
        arguments.append(" --out out.fasta");

        //System.out.println(arguments.toString());

        JobInputType jobIn = new JobInputType(arguments.toString(), //argList, 
                1, //numProcs, 
                null, //userEmail, 
                null, //password, 
                null, //wallClockTime, 
                null, //inputFile, 
                null, //extractInputs, 
                null);//sendNotification);

        //Non Blocking
        JobSubOutputType jobOut;
        try {
            jobOut = servicePort.launchJob(jobIn);
            jobID = jobOut.getJobID();
            return jobID;
        } catch (RemoteException e) {
            e.printStackTrace();
            return null;
        }

        /*
        //Blocking
        JobOutputType jobOut = servicePort.launchJobBlocking(jobIn).getJobOut();
            
        OutputFileType outFile = null;
        for(OutputFileType tmp : jobOut.getOutputFile()){
           if(tmp.getUrl().toString().endsWith("result.txt"))
        outFile = tmp;
        }
            
        if(outFile != null){
           //System.out.println(outFile.getUrl().toString());
           return outFile.getUrl().toString();
        }
        else{
           return null;
        }
        */
    }

}