UGEOutputParser.java

/**
 *
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied.  See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */
package org.apache.airavata.gfac.impl.job;

import org.apache.airavata.gfac.core.GFacException;
import org.apache.airavata.gfac.core.SSHApiException;
import org.apache.airavata.gfac.core.cluster.OutputParser;
import org.apache.airavata.model.status.JobState;
import org.apache.airavata.model.status.JobStatus;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

public class UGEOutputParser implements OutputParser {
    private static final Logger log = LoggerFactory.getLogger(PBSOutputParser.class);
    public static final String JOB_ID = "jobId";

	public String parseJobSubmission(String rawOutput) {
		log.debug(rawOutput);
		if (rawOutput != null && !rawOutput.isEmpty() && !isJobSubmissionFailed(rawOutput)) {
			String[] info = rawOutput.split("\n");
			String lastLine = info[info.length - 1];
			return lastLine.split(" ")[2]; // In PBS stdout is going to be directly the jobID
		} else {
			return "";
		}
	}

    @Override
    public boolean isJobSubmissionFailed(String rawOutput) {
        Pattern pattern = Pattern.compile("Rejecting");
        Matcher matcher = pattern.matcher(rawOutput);
        return matcher.find();
    }

    public JobStatus parseJobStatus(String jobID, String rawOutput) {
        Pattern pattern = Pattern.compile("job_number:[\\s]+" + jobID);
        Matcher matcher = pattern.matcher(rawOutput);
        if (matcher.find()) {
	        return new JobStatus(JobState.QUEUED); // fixme; return correct status.
        }
	    return new JobStatus(JobState.UNKNOWN);
    }

    public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput) {
        log.debug(rawOutput);
        String[] info = rawOutput.split("\n");
        int lastStop = 0;
        for (String jobID : statusMap.keySet()) {
            for(int i=lastStop;i<info.length;i++){
               if(jobID.split(",")[0].contains(info[i].split(" ")[0]) && !"".equals(info[i].split(" ")[0])){
                   // now starts processing this line
                   log.info(info[i]);
                   String correctLine = info[i];
                   String[] columns = correctLine.split(" ");
                   List<String> columnList = new ArrayList<String>();
                   for (String s : columns) {
                       if (!"".equals(s)) {
                           columnList.add(s);
                       }
                   }
                   lastStop = i+1;
                   if ("E".equals(columnList.get(4))) {
                       // There is another status with the same letter E other than error status
                       // to avoid that we make a small tweek to the job status
                       columnList.set(4, "Er");
                   }
	               statusMap.put(jobID, new JobStatus(JobState.valueOf(columnList.get(4))));
	               break;
               }
            }
        }
    }

    @Override
    public String parseJobId(String jobName, String rawOutput) throws GFacException {
        if (jobName.length() > 10) {
            jobName = jobName.substring(0, 10);
        }
        Pattern pattern = Pattern.compile("(?<" + JOB_ID + ">\\S+)\\s+\\S+\\s+(" + jobName + ")");
        Matcher matcher = pattern.matcher(rawOutput);
        if (matcher.find()) {
            return matcher.group(JOB_ID);
        }
        return null;
    }


}