FileLinkerLine.java

package net.sourceforge.seqware.pipeline.plugins.filelinker;

import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class FileLinkerLine {

    private static final Logger LOG = LoggerFactory.getLogger(FileLinkerLine.class);

    private String sequencerRun;
    private String sample;
    private Integer lane;
    private Integer seqwareAccession;
    private String fileStatus;
    private String mimeType;
    private String filename;
    private Long size;
    private String md5sum;

    public String getSequencerRun() {
        return sequencerRun;
    }

    public void setSequencerRun(String sequencerRun) {
        this.sequencerRun = sequencerRun;
    }

    public String getSample() {
        return sample;
    }

    public void setSample(String sample) {
        this.sample = sample;
    }

    public Integer getLane() {
        return lane;
    }

    public void setLane(Integer lane) {
        this.lane = lane;
    }

    public Integer getSeqwareAccession() {
        return seqwareAccession;
    }

    public void setSeqwareAccession(Integer seqwareAccession) {
        this.seqwareAccession = seqwareAccession;
    }

    public String getFileStatus() {
        return fileStatus;
    }

    public void setFileStatus(String fileStatus) {
        this.fileStatus = fileStatus;
    }

    public String getMimeType() {
        return mimeType;
    }

    public void setMimeType(String mimeType) {
        this.mimeType = mimeType;
    }

    public String getFilename() {
        return filename;
    }

    public void setFilename(String filename) {
        this.filename = filename;
    }

    public Long getSize() {
        return size;
    }

    public void setSize(Long size) {
        this.size = size;
    }

    public String getMd5sum() {
        return md5sum;
    }

    public void setMd5sum(String md5sum) {
        this.md5sum = md5sum;
    }

    public void setLaneString(String laneString) {
        if (!StringUtils.isBlank(laneString)) {
            try {
                setLane(Integer.parseInt(laneString));
            } catch (NumberFormatException e) {
                // log.error("The lane [{}] is not a valid integer value. {}", laneString, e);
                // this can be ignored, FileLinker does not require lane
            }
        }
    }

    public void setSeqwareAccessionString(String seqwareAccessionString) {
        if (!StringUtils.isBlank(seqwareAccessionString)) {
            try {
                setSeqwareAccession(Integer.parseInt(seqwareAccessionString));
            } catch (NumberFormatException e) {
                LOG.error("The SeqWare accession number [{}] is not a valid integer value. {}", seqwareAccessionString, e);
            }
        }
    }

    public void setSizeString(String sizeString) {
        if (!StringUtils.isBlank(sizeString)) {
            try {
                setSize(Long.parseLong(sizeString));
            } catch (NumberFormatException e) {
                LOG.error("The size [{}] is not a valid integer value. {}", sizeString, e);
            }
        }
    }

    public boolean hasRequiredValues() {
        return seqwareAccession != null && !StringUtils.isBlank(mimeType) && !StringUtils.isBlank(filename);
    }

    @Override
    public String toString() {
        StringBuilder sb = new StringBuilder();
        sb.append("FileLinkerLine:{");
        sb.append("sequencerRun=").append(sequencerRun);
        sb.append(", sample=").append(sample);
        sb.append(", lane=").append(lane);
        sb.append(", seqwareAccession=").append(seqwareAccession);
        sb.append(", fileStatus=").append(fileStatus);
        sb.append(", mimeType=").append(mimeType);
        sb.append(", filename=").append(filename);
        sb.append(", size=").append(size);
        sb.append(", md5sum=").append(md5sum);
        sb.append("}");
        return sb.toString();
    }

}